New Results

Structural Basis of Mitochondrial Receptor Binding and GTP-Driven Conformational Constriction by Dynamin-Related Protein 1

Raghav Kalia, Ray Yu-Ruei Wang, Ali Yusuf, Paul V. Thomas, David A. Agard, Janet M. Shaw, Adam Frost
doi: https://doi.org/10.1101/172809

Abstract

Mitochondrial inheritance, genome maintenance, and metabolic adaptation all depend on organelle fission by Dynamin-Related Protein 1 (DRP1) and its mitochondrial receptors. DRP1 receptors include the paralogs Mitochondrial Dynamics 49 and 51 (MID49/MID51) and Mitochondrial Fission Factor (MFF), but the mechanisms by which these proteins recruit DRP1 and regulate its activities are unknown. Here we present a cryoEM structure of human, full-length DRP1 bound to MID49 and an analysis of structure- and disease-based mutations. We report that GTP binding allosterically induces a remarkable elongation and rotation of the G-domain, Bundle-Signaling Element (BSE) and connecting hinge loops of DRP1. In this nucleotide-bound conformation, a distributed network of multivalent interactions promotes DRP1 copolymerization into a linear filament with MID49, MID51 or both. Subsequent GTP hydrolysis and exchange within the filament leads to receptor dissociation, shortening through disassembly, and concomitant curling of DRP1 oligomers into closed rings. The dimensions of the closed DRP1 rings are consistent with DRP1-constricted mitochondrial tubules observed in human cells. These structures are the first views of full-length, receptor- and nucleotide-bound dynamin-family GTPases and—in comparison with nucleotide-free crystal structures—teach us how these molecular machines perform mechanical work through nucleotide-driven allostery.

Introduction

Pioneering work in yeast and other model systems revealed that fragmentation of the mitochondrial reticulum disperses units of the organelle during cell division1–3, coordinates morphological adaptation with metabolic demand4–7, and quarantines damaged units for turnover8–10. Recent work also led to the discovery of the role mitochondrial fission plays in regulated cell death pathways11–19, brain development and synaptic function20–23, and how certain pathogens disrupt these processes and hijack mitochondrial resources24–26. Finally, there is a growing understanding of how interorganelle contacts between the ER and mitochondria initiate mitochondrial fission27,28, and how this process regulates mitochondrial genome duplication and integrity29,30. The master regulator that unites these processes across eukaryotic evolution is the membrane-remodeling GTPase DRP14,7,31–37.

DRP1 is necessary but not sufficient for mitochondrial fission because receptor proteins must recruit the enzyme to the Outer Mitochondrial Membrane (OMM). In mammals, these include the paralogs MItochondrial Dynamics proteins MID49 and MID51 or the Mitochondrial Fission Factor, MFF 32,35,38–41. Following receptor-dependent recruitment, DRP1 assembles into polymers that encircle mitochondria and, through still poorly understood mechanisms, channels energy from GTP binding, hydrolysis, and nucleotide exchange into a mechanochemical constriction13,41–46. In addition to DRP1 and its OMM receptors, a recent study revealed that a second member of the dynamin-family of GTPases, dynamin-2, enacts the final fission event downstream of DRPI-driven constriction of a mitochondrial tubule47. Thus, mitochondrial division is a stepwise reaction regulated by DRP1 receptor binding, oligomerization and nucleotide-dependent conformational dynamics.

We and others have reported that the OMM receptors MFF or MID49/51 are independently sufficient to recruit DRP1 in order to divide mitochondria38,39,41,48. We also reported that MID49/51 can coassemble with DRP1 forming a copolymer with a dramatically different morphology than reported for dynamin-family members41. While these results suggest that an adaptor protein could alter the architecture of a dynamin polymer to facilitate a mitochondria-specific activity, the architecture and functions of this coassembly remain unclear.

Here, we report the structural basis of DRP1 coassembly with MID49/MID51. Our cryoEM structure reveals how nucleotide binding to the G-domain induces conformational changes that allosterically propagate through the BSE to open and elongate DRP1 and thereby expose multiple receptor-binding surfaces. MID49/51 binding stabilizes a specific alignment of DRP1 tetramers to nucleate polymerization of a linear co-filament. Then, in a path-dependent reaction, we show how GTP hydrolysis and nucleotide exchange lead to conformational constriction by the polymer. Specifically, when DRP1 subunits within the cofilament exchange and hydrolyze nucleotide, they dissociate from MID49/51 receptors and the entire polymer dynamically shortens and curls into a closed ring. Analysis of structure-based and disease-causing mutations indicate that allosterically driven rearrangements of the stalk helices—and the critical L1NS loop—support curling from linear strings into constricted rings following receptor dissociation.

Results and Discussion

To date, many structural studies of dynamin-family proteins have relied upon mutated or truncated constructs to facilitate crystallization. We purified wild-type, full-length human DRP1 including the N-terminal GTPase domain (G-domain), Bundle Signaling Element (BSE), and four-helix bundle known as the stalk (Fig. 1a). This construct also contained the lipid binding ~100 amino acid region referred to as the variable domain (VD) that sits between the third and fourth alpha helices of the stalk, analogous to the Pleckstrin Homology (PH) domain found in endocytic dynamin proteins. A crystal structure of a nucleotide-free and truncated DRP1 mutant revealed the organization of these domains and an overall similarity with the structure of nucleotide-free endocytic dynamin42,49,50. We also purified soluble truncations of MID49 and MID51 engineered to lack their N-terminal transmembrane anchors but include the cytoplasmic nucleotidyltransferase-like domain and the “Dynamin Recruitment Region” (DRR) required for DRP1 binding (Fig 1a)38,51–54.

Figure 1:
Figure 1: Architecture of the DRP1-MID49 linear filament:

(a) DRP1 and MID49 domain arrangements. (b) Density map and atomic models for DRP1 and MID49126-454. Green: G-domain, Red: Bundle Signaling Element (BSE), Purple: Stalk, Blue: MID49, Yellow: Dynamin Recruitment Region (DRR) of MID49. (c) Each DRP1 chain contacts four different MID49 molecules, as numbered. (d) MID-interaction surfaces 1 and 2. Green ribbons on either side of the DRR come from two separate G-domains, and the residues involved in a key salt bridge for MID-interaction surface 1 are shown as sticks. (e) Rotated view of MID-interaction surface 3. Disease-associated DRP1 residue G362 (arrow) supports the conformation of the L1NS loop essential for linear copolymerization with MID receptors. (f) Rotated view of MID-interaction surface 4 and the L2S loop.

Incubating equimolar ratios of DRP1 with soluble MID49126-454, MID51132-463, or both proteins together, in the presence of GTP resulted in cofilament assembly (Extended Data Figs. 1–2). We focused on the filaments formed with MID49126-454 in the presence of the non-hydrolyzable analog GMPPCP and determined their structure from cryoEM images (Extended Data Figs. 3–9 and Table 1). 3D reconstruction resolved elongated DRP1 dimers bound stoichiometrically to MID49126-454, without assignable density for the variable domain (Fig. 1b, Extended Data Fig. 4). Surprisingly, each chain of DRP1 bound MID49 at four different sites, and each MID49 in turn bound four DRP1 molecules to yield a vast and highly avid interaction network (Figs. 1b-c, Extended Data Figs. 4 and 8). MID49 binding to four separate DRP1 molecules stabilized a linear arrangement of inter-DRP1 interfaces reminiscent of those observed for other dynamin-family proteins by X-ray crystallography (Fig. 1b, Extended Data Figs. 4 and 8)42,49,50,55–57.

Extended data figure 1:
Extended data figure 1:

DRP1 assembly states visualized with negative stain electron microscopy in the presence of different guanine nucleotides and stoichiometric MID49126-454 ([2μM] for both proteins). Bars = 100nm.

Extended data figure 2:
Extended data figure 2:

MID49126-454 and MID51132-463 form indistinguishable assemblies with DRP1 by negative stain electron microscopy. (a) DRP1 plus MID49126-454 and GMPPCP; (b) DRP1 plus MID51132-463 and GMPPCP, (c) DRP1 plus both MID49 and MID51. Bars = 100nm.

Extended data figure 3:
Extended data figure 3:

CryoEM imaging and reconstruction. (a) An electron cryo-micrograph of DRP1-MID49126-454 filaments formed with GMPPCP. Inset shows a representative 2D class average. Bar =100nm, Inset bar =10nm. (b) Oblique cross-section of the 3D reconstruction and the distribution of views determined during helical reconstruction. DRP1 density is rendered in grey, MID49 in golden yellow.

Extended data figure 4:
Extended data figure 4:

Raw particle numbers and workflow for the reconstruction protocol and imposition of symmetries. DRP1 density is rendered in grey, MID49 in golden yellow.

Extended data figure 5:
Extended data figure 5:

Local resolution estimates computed by Resmap25. (a) Histogram of voxels values, and (b) Heat map of local resolution estimates displayed for a cross-section through the reconstruction.

Extended data figure 6:
Extended data figure 6:

Fourier Shell Correlation plots for (a) the half-maps with and without imposed symmetry; and (b) model-to-map correlations for the averaged as well as each subregion of the structure using the atomic coordinates and B-factors determined using Rosetta.

Extended data figure 7:
Extended data figure 7:

Modeling of human MID49. (a) Sequence alignment between human and mouse MID49 sequences. (b) Overlay of the homology model of human MID49126-454 (blue, with yellow DRR, ribbon) modeled within the cryoEM density versus the mouse MID49 crystal structure (PDB ID: 4WOY, grey ribbon)6.

Extended data figure 8:
Extended data figure 8:

Rosetta refinement. (a) Symmetric unit of the filament with 8 chains of DRP1 and 8 chains of MID49 refined using Rosetta to enforce symmetry and account for all possible inter-molecular interfaces. (b) Atomic B-factors for the DRP1 and MID49 models (ribbon) and bound GMPPCP (space filling).

MID49’s DRR motif occupied the space between two neighboring G-domains and contacted both via MID-interaction interfaces 1 and 2 (buried surface areas of ~530Å2 and ~200 Å2, respectively, see Fig. 1b-d). The precise spacing required for this bivalent G-domain interaction explains why previous mutagenesis efforts suggested that the size and topology of the β4–α4 loop, rather than its exact sequence (which differs between MID49 and MID51) are critical determinants of binding. Single point mutations within this loop for MID49 and MID51 did not disrupt binding, while mutations that altered the length, topology or positioning of the loop did51,52,54. We found that mutating conserved DRP1 residues involved in interface 1—the energetically most significant interface—did prevent coassembly. Specifically, the D190A mutation should neutralize an interface 1 salt bridge and the D221A mutation should alter the conformation of an interface 1 loop (Fig. 1d). We observed that both mutants prevented assembly with MID49 and altered DRP1’s self-assembly properties (Extended Data Figs. 10–12).

Extended data figure 9:
Extended data figure 9:

Examples of model fitting to B-factor sharpened density for (a) a helix from the DRP1 stalk, (b) the backbone of the L1NS loop, and (c) a helix and loop from MID49.

Extended data figure 10:
Extended data figure 10:

DRP1 assembly and coassembly reactions with GMPPCP for (a) DRP1D190A alone, (b) DRP1D190A+MID49, (c) DRP1D221A alone, and (d) DRP1D221A+MID49. Bars = 100nm.

Unexpectedly, MID49 also made contact with the stalk loops of a third and fourth DRP1 molecule through MID-interaction interfaces 3 and 4 (buried surface areas of ~450Å2 and ~230Å2, respectively, Fig. 1c, e, and f). The loops involved in both interaction interfaces 3 and 4 determine the assembly properties of higher-order dynamin-family oligomers 42,49,50,55–57. MID-interaction surface 3, in particular, harbors the conserved loop L1NS and is the site of multiple disease alleles that lead to elongated mitochondrial morphology, including G362D and G363D (Fig. 1e, Extended Data Figs. 10–11 and 58–60). Prior work has also established that this loop comprises part of the intra-molecular PH domain binding site for the soluble state of endocytic dynamin tetramers (Extended Data Fig. 13)57, and is a determinant of conformational heterogeneity for these and other dynamin-family proteins55,57,61. The presence of disease alleles near this interface suggests that these mutations may compromise receptor interactions and that defects in the recruitment of DRP1 to mitochondria may contribute to pathogenesis. As discussed below, we found that the G362D mutant (Fig. 1e) failed to coassemble with MID49 and displayed altered assembly and conformational properties (Extended Data Figs. 12–15).

Extended data figure 11:
Extended data figure 11:

Multiple sequence alignment of the regions near and including the DRP1 residues mutated in this study: D190, D221 and G362. The residue numbers apply to human DRP1, isoform 2 (UNIPROT identifier: O00429-3 also known as DLP1a).

Extended data figure 12:
Extended data figure 12:

Size exclusion chromatography traces for DRP1 wild-type and mutants used in the study. (a) Comparison between wild type (WT) versus DRP1G362D, (b) WT versus DRP1D221A, and (c) WT versus DRP1D190A. (d) Standards for molecular weight comparison.

Understanding the allosteric coupling between nucleotide binding, hydrolysis or exchange and the conformational repertoire of dynamin-family GTPases remains an unmet challenge62,63. We observed that the GMPPCP-bound G-domains and the BSE of DRP1 adopt strikingly different conformations in the cryoEM density compared to the nucleotide-free crystal structure42. In addition to other nucleotide-induced conformational changes within the G-domain, the most salient are the closing of the G2/switch-1 loop to form a closed “lid” over the nucleotide (Figs. 2a-c). The closure of the switch-1 lid propagates through the adjacent beta sheet to push the α-helices of the BSE into an orthogonal position (Extended Data Movie 1). When evaluated in the context of a stalk interface-2 DRP1 dimer, this conformational change is an impressive 90° rotation of the G-domain and a 40Å translation toward the stalk (Fig. 2d, Extended Data Movies 2-3). Two of the three DRP1 surfaces that engage the DRR of MID49 (MID receptor interaction interfaces 1 and 2, Figs. 1–2) are inaccessible in the nucleotide-free state but become available for binding upon nucleotide-driven elongation (Fig. 2d, Extended Data Movies 2-3).

Figure 2:
Figure 2: Nucleotide-driven allosteric elongation of DRP1 exposes MID binding sites:

(a) nucleotide-free state of DRP1 G-domain and BSE as seen in a crystal structure (PDB ID:4BEJ). Arrow points to the G2/switch1 loop. (b) GMPPCP-bound G-domain-BSE conformation determined by cryoEM. (c) Overlay of A and B. Curved arrows highlight the closing of G2/switch 1 “lid” and the opening of the BSE “wrist”. (d) Global conformational change induced by nucleotide binding. Rotation and translation of the G-domain and BSE elongates the dimer and exposes MID-interaction surfaces 1 and 2 (annotated on separate monomers for clarity). The surfaces of the G-domains that engage MID receptors are rendered orange in the nucleotide-bound and elongated conformation.

Since DRP1’s ability to polymerize into linear filaments with MID49 or MID51 depended on non-hydrolyzable GTP analogs, we next evaluated the dynamics of these filaments in the presence of hydrolyzable GTP. Following copolymerization in the presence of the non-hydrolyzable analog, we exchanged GMPPCP for GTP through dialysis and followed the reaction using negative stain transmission electron microscopy at sequential time points until the GTP was exhausted. We observed that the linear DRP1-MID49 cofilaments disassembled into small oligomers upon complete hydrolysis to GDP and exhibited a fascinating dynamic instability at intermediate time points (Fig. 3). Specifically, the long and linear filaments seen at early time points disassembled into shorter, curling oligomers that—upon reaching a reproducibly narrow range of lengths—spontaneously closed into constricted rings that were remarkably uniform in diameter (Fig. 3).

Figure 3:
Figure 3: Dynamic instability of the DRP1-MID49 linear assembly and curling into closed DRP1 rings:

(a) DRP1-MID49126-454 linear filaments copolymerized with GMPPCP. (b-c) Subsequent exchange into GTP leads to partial disassembly and curling into closed rings. (d) GTP exhaustion leads to complete oligomer disassembly. Bars=100nm.

In a separate but related experiment, we evaluated the assembly properties of the DRP1 mutant G362D with and without MID49126-454. As described above, this disease-associated residue sits at the base of the L1NS loop that forms part of the third interface with MID49 (Figs. 1c, 1e, Extended Data Fig. 13). We found that DRP1G362D purified as a nearly monodisperse and stable dimer, rather than a mix of tetramers and higher order species observed for the wild-type, full-length protein (Extended Data Fig. 12). In addition, DRP1G362D exclusively formed rings, not filaments, with or without MID49126-454 and in the presence of GMPPCP or GTP (Fig. 4a, Extended Data Figs. 14–15). These rings resembled those observed with wild-type DRP1 in all respects except that the wild-type protein only formed closed rings from the pre-formed linear MID49 copolymers through the path-dependent reaction described above (Fig. 3 versus Fig. 4). Using the non-hydrolyzable GTP analog GMPPCP with the DRP1G362D rings also improved structural homogeneity, presumably because the wild-type rings remain dynamic and eventually disassembled in the presence of GTP upon complete hydrolysis to GDP (Fig. 3).

Extended data figure 13:
Extended data figure 13:

Structural similarities between the third DRP1-MID49 interaction interface that includes the L1NS loop and the interaction between the Pleckstrin Homology (PH) domain and the stalk of Dynamin-3 (PDB ID:5A3F)26. (a) DRP1-MID49 interaction at MIDinteraction interface 3, (b) the PH domain bound to the stalk of Dynamin-3, and (c) Overlay of a and b.

Extended data figure 14:
Extended data figure 14:

DRP1G362D assembly and coassembly reactions with GMPPCP or GTP. DRP1G362D forms rings but not linear filaments without MID49 (a,c); and with MID49 present (b,d); with GMPPCP (a-b); or with GTP (c-d). Bars = 100 nm.

Extended data figure 15:
Extended data figure 15:

DRP1G362D forms 12-dimer closed rings. (a) 2D class average of the rings; (b) 2D class average of infrequent, orthogonal or “side” views used as a constraint during model building; (c) “top” and (d) “side” projections of the model; (e) “top” and (f) “side” views of the final model rendered as ribbons. Bars =100Å. Green: G-domain, Red: Bundle Signaling Element (BSE), Purple: Stalk region.

Figure 4:
Figure 4: DRP1G362D cannot bind MID49 and forms rings exclusively with GMPPCP or GTP.

(a) CryoEM micrograph of DRP1G362D rings. (b) 2D class average of the predominant closed ring that comprises 12 DRP1 dimers. (c) 2D class average of a quarter of the ring revealing the secondary structure elements of the “X”-shaped DRP1 dimer. (d) 3D model of the closed ring. (e) Comparison between DRP1 tetramers observed in the nucleotide-free state (top, PDB ID:4BEJ), the GMPPCP and MID49126-454-bound linear state (middle), and the bent conformation modeled for the rings. Bar for (a) = 30nm, for (b, c) =100Å.

We imaged the DRP1G362D rings using cryoEM and used 2D class averages of the predominant 12-dimer closed ring to model the architectural differences between the linear filaments and the closed rings (Fig. 4, Extended Data Fig. 14–15). To account for the projected ring density, the G-domain and the BSE of DRP1 must move even further down toward the stalks. Moreover, while stalk interface-2 remains constant—as revealed by the X-shaped projected dimer (Fig. 4c)—the curvature of the ring dictates that stalk interfaces 1 and 3 must be extensively remodeled to allow a ~30 degree bending per dimer in comparison with the linear DRP1-MID49 copolymer (Fig. 4d, Extended Data Fig. 15, Movie 4). We did not observe any density for MID49 in the wild-type rings that form by curling of the MID49-DRP1 cofilament in the presence of GTP, nor in our higher-resolution analysis of the DRP1G362D rings that form with or without MID49 present (Fig. 4b-c, Extended Data Fig. 14–15).

We note that even the most constricted form of the closed ring is insufficient to drive complete mitochondrial fission because the inner diameter is only ~16nm. This length suggests that a constricted membrane tubule would be stable and that the structures we have observed in vitro could correspond with the highly-constricted but pre-fission state observed in living cells when another dynamin-family protein, the primarily endocytic dynamin-2, is depleted47. Thus, initial constriction by DRP1 may stabilize the high degree of membrane curvature that is suitable, perhaps even tuned, for the recruitment and final fission event catalyzed by additional dynamin-family enzymes.

Together, these findings establish four conceptual advances. First, our cryoEM structure revealed how receptor proteins like MID49/MID51 recruit and stabilize a specific nucleotide-bound conformation of DRP1 and nucleate polymerization of a cofilament. We speculate that the nearly linear properties of this polymer have adapted to encircle low-curvature mitochondrial tubules. The selective stabilization of this open, elongated conformation of DRP1 within the MID receptor cofilament explains why overexpression of the MID receptors inhibits mitochondrial fission39. Second, analysis of the MID49-DRP1 copolymer exposed how nucleotide binding induces an impressive conformational rearrangement to expose a network of multi-valent receptor binding sites. We now understand these nucleotide-driven allosteric transformations in detail and in the context of full-length and oligomeric DRP1. Third, a path-dependent constriction reaction revealed intrinsic GTP-dependent DRP1 properties that are reminiscent of microtubule dynamic instability64. In this reaction, nucleotide exchange and hydrolysis led to MID49/51 receptor dissociation, disassembly from the ends of the linear filament, and concomitant curling of the shortened filaments into closed rings. Fourth and finally, analysis of a disease mutant in the L1NS loop, DRP1G362D, exposed this loop as a vital determinant of mitochondrial receptor binding and the dynamic inter-stalk interactions that govern oligomer architecture and the ability of dynamin proteins to perform mechanical work.

Author Contributions

R.K., J.S. and A.F. conceived of the study. R.K., R.W., A.Y. and P.T. performed all experiments. R.K., R.W. and A.F. performed the computational analyses. All authors evaluated the results and edited the manuscript. R.K. and A.F. wrote the manuscript with input from all of the authors.

Data Accessibility

All of the cryoEM density maps associated with this study have be deposited in the EMDB with accession numbers EMD-8874(PROC). The atomic coordinates have been deposited in the PDB as 5WP9(PROC).

Extended data movie Legends

Extended data movie 1: Nucleotide-induced conformational changes in the G-domain and Bundle Signaling Element (BSE).

Extended data movie 2: Nucleotide-induced conformational changes in the G-domain and Bundle Signaling Element (BSE) in the context of a full-length DRP1 dimer (“side” view).

Extended data movie 3: Nucleotide-induced conformational changes in the G-domain and Bundle Signaling Element (BSE) in the context of a full-length DRP1 dimer (“top” view).

Extended data movie 4: MID receptors engage a specific nucleotide-bound conformation of DRP1 tetramers and promote formation of a linear copolymer. Subsequent nucleotide hydrolysis and exchange promotes receptor dissociation and tetramer bending in the closed rings.

1 Overall quality at a glance ⓘ

The following experimental techniques were used to determine the structure:

ELECTRON MICROSCOPY

The reported resolution of this entry is unknown.

Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown in the following graphic. The table shows the number of entries on which the scores are based.

Figure

The table below summarises the geometric issues observed across the polymeric chains. The red, orange, yellow and green segments on the bar indicate the fraction of residues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria. A grey segment represents the fraction of residues that are not modelled. The numeric value for each fraction is indicated below the corresponding segment, with a dot representing fractions <=5%

2 Entry composition ⓘ

There are 2 unique types of molecules in this entry. The entry contains 116960 atoms, of which 59040 are hydrogens and 0 are deuteriums.

In the tables below, the AltConf column contains the number of residues with at least one atom in alternate conformation and the Trace column contains the number of residues modelled with at most 2 atoms.

3 Residue-property plots ⓘ

These plots are drawn for all protein, RNA and DNA chains in the entry. The first graphic for a chain summarises the proportions of the various outlier classes displayed in the second graphic. The second graphic shows the sequence view annotated by issues in geometry. Residues are colorcoded according to the number of geometric quality criteria for which they contain at least one outlier: green = 0, yellow = 1, orange = 2 and red = 3 or more. Stretches of 2 or more consecutive residues without any outlier are shown as a green connector. Residues present in the sample, but not in the model, are shown in grey.

Figure
Figure
Figure

4 Experimental information ⓘ

5 Model quality ⓘ

5.1 Standard geometry ⓘ

Bond lengths and bond angles in the following residue types are not validated in this section: GCP, MG

The Z score for a bond length (or angle) is the number of standard deviations the observed value is removed from the expected value. A bond length (or angle) with |Z| > 5 is considered an outlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (or angles).

There are no bond length outliers.

There are no bond angle outliers.

There are no chirality outliers.

There are no planarity outliers.

5.2 Too-close contacts ⓘ

In the following table, the Non-H and H(model) columns list the number of non-hydrogen atoms and hydrogen atoms in the chain respectively. The H(added) column lists the number of hydrogen atoms added and optimized by MolProbity. The Clashes column lists the number of clashes within the asymmetric unit, whereas Symm-Clashes lists symmetry related clashes.

The all-atom clashscore is defined as the number of clashes found per 1000 atoms (including hydrogen atoms). The all-atom clashscore for this structure is 2.

All (249) close contacts within the same asymmetric unit are listed below, sorted by their clash magnitude.

View this table:

There are no symmetry-related clashes.

5.3 Torsion angles ⓘ

5.3.1 Protein backbone ⓘ

In the following table, the Percentiles column shows the percent Ramachandran outliers of the chain as a percentile score with respect to all PDB entries followed by that with respect to all EM entries.

The Analysed column shows the number of residues for which the backbone conformation was analysed, and the total number of residues.

All (96) Ramaehandran outliers are listed below:

View this table:

5.3.2 Protein sidechains ⓘ

In the following table, the Percentiles column shows the percent sidechain outliers of the chain as a percentile score with respect to all PDB entries followed by that with respect to all EM entries.

The Analysed column shows the number of residues for which the sidechain conformation was analysed, and the total number of residues.

All (24) residues with a non-rotamerie sideehain are listed below:

Some sidechains can be flipped to improve hydrogen bonding and reduce clashes. There are no such sidechains identified.

5.3.3 RNA ⓘ

There are no RNA molecules in this entry.

5.4 Non-standard residues in protein, DNA, RNA chains ⓘ

There are no non-standard protein/DNA/RNA residues in this entry.

5.5 Carbohydrates ⓘ

There are no carbohydrates in this entry.

5.6 Ligand geometry ⓘ

There are no ligands in this entry.

5.7 Other polymers ⓘ

There are no such residues in this entry.

5.8 Polymer linkage issues ⓘ

The following chains have linkage breaks:

All chain breaks are listed below:

Acknowledgments

We thank Michael Braunfeld, Cameron Kennedy, David Bulkley, and Alexander Myasnikov and the UCSF Center for Advanced CryoEM, which is supported in part from NIH grants S10OD020054 and 1S10OD021741 and the Howard Hughes Medical Institute. We also thank the QB3 shared cluster and NIH grant 1S10OD021596-01, Jean-Paul Armache, Nathaniel Talledge for microscopy advice, and Charles Greenberg for consulting on structural modeling. This work was further supported by a Faculty Scholar grant from the Howard Hughes Medical Institute (A.F.), the Searle Scholars Program (A.F.), NIH grant 1DP2GM110772-01 (A.F.), NIH grants GM53466 and GM84970 (J.S.), and the Howard Hughes Medical Institute (R.W., J.S., D.A.). A.F. is a Chan Zuckerberg Biohub investigator.

References

  1. ↵
    Mishra, P. & Chan, D. C. Mitochondrial dynamics and inheritance during cell division, development and disease. Nature reviews. Molecular cell biology 15, 634–646, doi10.1038/nrm3877 (2014).
    OpenUrlCrossRefPubMed
  2. Jourdain, I., Gachet, Y. & Hyams, J. S. The dynamin related protein Dnm1 fragments mitochondria in a microtubule-dependent manner during the fission yeast cell cycle. Cell Motil Cytoskeleton 66, 509–523, doi10.1002/cm.20351 (2009).
    OpenUrlCrossRefPubMed
  3. ↵
    Kanfer, G. & Kornmann, B. Dynamics of the mitochondrial network during mitosis. Biochem Soc Trans 44, 510–516, doi10.1042/BST20150274 (2016).
    OpenUrlAbstract/FREE Full Text
  4. ↵
    Toyama, E. Q. et al. Metabolism. AMP-activated protein kinase mediates mitochondrial fission in response to energy stress. Science (New York, N.Y.) 351, 275–281, doi10.1126/science.aab4138 (2016).
    OpenUrlAbstract/FREE Full Text
  5. Roy, M., Reddy, P. H., Iijima, M. & Sesaki, H. Mitochondrial division and fusion in metabolism. Current opinion in cell biology 33, 111–118, doi10.1016/j.ceb.2015.02.001 (2015).
    OpenUrlCrossRefPubMed
  6. Picard, M., Juster, R. P. & McEwen, B. S. Mitochondrial allostatic load puts the ’gluc’ back in glucocorticoids. Nat Rev Endocrinol 10, 303–310, doi10.1038/nrendo.2014.22 (2014).
    OpenUrlCrossRefPubMed
  7. ↵
    Mishra, P. & Chan, D. C. Metabolic regulation of mitochondrial dynamics. The Journal of cell biology 212, 379–387, doi10.1083/jcb.201511036 (2016).
    OpenUrlAbstract/FREE Full Text
  8. ↵
    Twig, G. et al. Fission and selective fusion govern mitochondrial segregation and elimination by autophagy. Embo J 27, 433–446, doi10.1038/sj.emboj.7601963 (2008).
    OpenUrlAbstract/FREE Full Text
  9. Frank, M. et al. Mitophagy is triggered by mild oxidative stress in a mitochondrial fission dependent manner. Biochim Biophys Acta 1823, 2297–2310, doi10.1016/j.bbamcr.2012.08.007 (2012).
    OpenUrlCrossRefPubMedWeb of Science
  10. ↵
    Mao, K. & Klionsky, D. J. Mitochondrial fission facilitates mitophagy in Saccharomyces cerevisiae. Autophagy 9, 1900–1901, doi10.4161/auto.25804 (2013).
    OpenUrlCrossRefPubMedWeb of Science
  11. ↵
    Chan, D. C. Fusion and fission: interlinked processes critical for mitochondrial health. Annu Rev Genet 46, 265–287, doi10.1146/annurev-genet-110410-132529 (2012).
    OpenUrlCrossRefPubMedWeb of Science
  12. ↵
    Lee, H. & Yoon, Y. Mitochondrial fission: regulation and ER connection. Mol Cells 37, 89–94, doi10.14348/molcells.2014.2329 (2014).
    OpenUrlCrossRef
  13. ↵
    van der Bliek, A. M., Shen, Q. & Kawajiri, S. Mechanisms of mitochondrial fission and fusion. Cold Spring Harb Perspect Biol 5, doi:10.1101/cshperspect.a011072 (2013).
    OpenUrlAbstract/FREE Full Text
  14. Sheridan, C. & Martin, S. J. Mitochondrial fission/fusion dynamics and apoptosis. Mitochondrion 10, 640–648, doi10.1016/j.mito.2010.08.005 (2010).
    OpenUrlCrossRefPubMedWeb of Science
  15. ↵
    Parone, P. A. & Martinou, J. C. Mitochondrial fission and apoptosis: an ongoing trial. Biochim Biophys Acta 1763, 522–530, doi10.1016/j.bbamcr.2006.04.005 (2006).
    OpenUrlCrossRefPubMed
  16. Youle, R. J. & Karbowski, M. Mitochondrial fission in apoptosis. Nature reviews. Molecular cell biology 6, 657–663, doi10.1038/nrm1697 (2005).
    OpenUrlCrossRefPubMedWeb of Science
  17. Perfettini, J. L., Roumier, T. & Kroemer, G. Mitochondrial fusion and fission in the control of apoptosis. Trends in cell biology 15, 179–183, doi10.1016/j.tcb.2005.02.005 (2005).
    OpenUrlCrossRefPubMedWeb of Science
  18. Oakes, S. A. & Korsmeyer, S. J. Untangling the web: mitochondrial fission and apoptosis. Dev Cell 7, 460–462, doi10.1016/j.devcel.2004.09.010 (2004).
    OpenUrlCrossRefPubMed
  19. ↵
    Frank, S. et al. The role of dynamin-related protein 1, a mediator of mitochondrial fission, in apoptosis. Dev Cell 1, 515–525 (2001).
    OpenUrlCrossRefPubMedWeb of Science
  20. ↵
    Ishihara, N. et al. Mitochondrial fission factor Drp1 is essential for embryonic development and synapse formation in mice. Nature cell biology 11, 958–966, doi10.1038/ncb1907 (2009).
    OpenUrlCrossRefPubMedWeb of Science
  21. Wakabayashi, J. et al. The dynamin-related GTPase Drp1 is required for embryonic and brain development in mice. Journal of Cell Biology 186, 805–816, doi10.1083/jcb.200903065 (2009).
    OpenUrlAbstract/FREE Full Text
  22. Kageyama, Y. et al. Parkin-independent mitophagy requires Drp1 and maintains the integrity of mammalian heart and brain. Embo J 33, 2798–2813, doi10.15252/embj.201488658 (2014).
    OpenUrlCrossRefPubMed
  23. ↵
    Schwarz, T. L. Mitochondrial trafficking in neurons. Cold Spring Harb Perspect Biol 5, doi:10.1101/cshperspect.a011304 (2013).
    OpenUrlAbstract/FREE Full Text
  24. ↵
    Chatel-Chaix, L. et al. Dengue Virus Perturbs Mitochondrial Morphodynamics to Dampen Innate Immune Responses. Cell Host Microbe 20, 342–356, doi10.1016/j.chom.2016.07.008 (2016).
    OpenUrlCrossRef
  25. Welsch, S. et al. Composition and three-dimensional architecture of the dengue virus replication and assembly sites. Cell Host Microbe 5, 365–375, doi10.1016/j.chom.2009.03.007 (2009).
    OpenUrlCrossRefPubMedWeb of Science
  26. ↵
    Kim, S. J. et al. Hepatitis B virus disrupts mitochondrial dynamics: induces fission and mitophagy to attenuate apoptosis. PLoS Pathog 9, e1003722, doi:10.1371/journal.ppat.1003722 (2013).
    OpenUrlCrossRefPubMed
  27. ↵
    Friedman, J. R. et al. ER tubules mark sites of mitochondrial division. Science (New York, N.Y.) 334, 358–362, doi10.1126/science.1207385 (2011).
    OpenUrlAbstract/FREE Full Text
  28. ↵
    Murley, A. et al. ER-associated mitochondrial division links the distribution of mitochondria and mitochondrial DNA in yeast. eLife 2, e00422, doi:10.7554/eLife.00422 (2013).
    OpenUrlCrossRefPubMed
  29. ↵
    Lewis, S. C., Uchiyama, L. F. & Nunnari, J. ER-mitochondria contacts couple mtDNA synthesis with mitochondrial division in human cells. Science (New York, N. Y.) 353, aaf5549, doi:10.1126/science.aaf5549 (2016).
    OpenUrlAbstract/FREE Full Text
  30. ↵
    Osman, C., Noriega, T. R., Okreglak, V., Fung, J. C. & Walter, P. Integrity of the yeast mitochondrial genome, but not its distribution and inheritance, relies on mitochondrial fission and fusion. Proc Natl Acad Sci U S A 112, E947–956, doi:10.1073/pnas.1501737112 (2015).
    OpenUrlAbstract/FREE Full Text
  31. ↵
    Chang, C. R. & Blackstone, C. Dynamic regulation of mitochondrial fission through modification of the dynamin-related protein Drp1. Ann N Y Acad Sci 1201, 34–39, doi10.1111/j.1749-6632.2010.05629.x (2010).
    OpenUrlCrossRefPubMedWeb of Science
  32. ↵
    Elgass, K., Pakay, J., Ryan, M. T. & Palmer, C. S. Recent advances into the understanding of mitochondrial fission. Biochim Biophys Acta 1833, 150–161, doi10.1016/j.bbamcr.2012.05.002 (2013).
    OpenUrlCrossRefPubMedWeb of Science
  33. Otera, H., Ishihara, N. & Mihara, K. New insights into the function and regulation of mitochondrial fission. Biochim Biophys Acta 1833, 1256–1268, doi10.1016/j.bbamcr.2013.02.002 (2013).
    OpenUrlCrossRefPubMedWeb of Science
  34. Prudent, J. et al. MAPL SUMOylation of Drp1 Stabilizes an ER/Mitochondrial Platform Required for Cell Death. Molecular cell 59, 941–955, doi10.1016/j.molcel.2015.08.001 (2015).
    OpenUrlCrossRefPubMed
  35. ↵
    Bui, H. T. & Shaw, J. M. Dynamin assembly strategies and adaptor proteins in mitochondrial fission. Current biology : CB 23, R891–899, doi:10.1016/j.cub.2013.08.040 (2013).
    OpenUrlCrossRef
  36. Koirala, S. et al. Molecular architecture of a dynamin adaptor: implications for assembly of mitochondrial fission complexes. The Journal of cell biology 191, 1127–1139, doi10.1083/jcb.201005046 (2010).
    OpenUrlAbstract/FREE Full Text
  37. ↵
    Bleazard, W. et al. The dynamin-related GTPase Dnm1 regulates mitochondrial fission in yeast. Nature cell biology 1, 298–304, doi10.1038/13014 (1999).
    OpenUrlCrossRefPubMedWeb of Science
  38. ↵
    Osellame, L. D. et al. Cooperative and independent roles of the Drp1 adaptors Mff, MiD49 and MiD51 in mitochondrial fission. Journal of cell science 129, 2170–2181, doi10.1242/jcs.185165 (2016).
    OpenUrlAbstract/FREE Full Text
  39. ↵
    Palmer, C. S. et al. Adaptor proteins MiD49 and MiD51 can act independently of Mff and Fis1 in Drp1 recruitment and are specific for mitochondrial fission. J Biol Chem 288, 27584–27593, doi10.1074/jbc.M113.479873 (2013).
    OpenUrlAbstract/FREE Full Text
  40. Palmer, C. S. et al. MiD49 and MiD51, new components of the mitochondrial fission machinery. EMBO reports 12, 565–573, doi10.1038/embor.2011.54 (2011).
    OpenUrlAbstract/FREE Full Text
  41. ↵
    Koirala, S. et al. Interchangeable adaptors regulate mitochondrial dynamin assembly for membrane scission. Proc Natl Acad Sci U S A 110, E1342–1351, doi:10.1073/pnas.1300855110 (2013).
    OpenUrlAbstract/FREE Full Text
  42. ↵
    Frohlich, C. et al. Structural insights into oligomerization and mitochondrial remodelling of dynamin 1-like protein. Embo J 32, 1280–1292, doi10.1038/emboj.2013.74 (2013).
    OpenUrlCrossRefPubMed
  43. Mears, J. A. et al. Conformational changes in Dnm1 support a contractile mechanism for mitochondrial fission. Nat Struct Mol Biol 18, 20–26, doi10.1038/nsmb.1949 (2011).
    OpenUrlCrossRefPubMed
  44. Ingerman, E. et al. Dnm1 forms spirals that are structurally tailored to fit mitochondria. The Journal of cell biology 170, 1021–1027, doi10.1083/jcb.200506078 (2005).
    OpenUrlAbstract/FREE Full Text
  45. Ferguson, S. M. & De Camilli, P. Dynamin, a membrane-remodelling GTPase. Nature reviews. Molecular cell biology 13, 75–88, doi10.1038/nrm3266 (2012).
    OpenUrlCrossRefPubMed
  46. ↵
    Daumke, O. & Praefcke, G. J. Invited review: Mechanisms of GTP hydrolysis and conformational transitions in the dynamin superfamily. Biopolymers 105, 580–593, doi10.1002/bip.22855 (2016).
    OpenUrlCrossRefPubMed
  47. ↵
    Lee, J. E., Westrate, L. M., Wu, H., Page, C. & Voeltz, G. K. Multiple dynamin family members collaborate to drive mitochondrial division. Nature 540, 139–143, doi10.1038/nature20555 (2016).
    OpenUrlCrossRefPubMed
  48. ↵
    Loson, O. C., Song, Z., Chen, H. & Chan, D. C. Fis1, Mff, MiD49, and MiD51 mediate Drp1 recruitment in mitochondrial fission. Molecular biology of the cell 24, 659–667, doi10.1091/mbc.E12-10-0721 (2013).
    OpenUrlAbstract/FREE Full Text
  49. ↵
    Faelber, K. et al. Crystal structure of nucleotide-free dynamin. Nature 477, 556–560, doi10.1038/nature10369 (2011).
    OpenUrlCrossRefPubMedWeb of Science
  50. ↵
    Ford, M. G., Jenni, S. & Nunnari, J. The crystal structure of dynamin. Nature 477, 561566, doi:10.1038/nature10441 (2011).
    OpenUrlCrossRef
  51. ↵
    Richter, V. et al. Structural and functional analysis of MiD51, a dynamin receptor required for mitochondrial fission. The Journal of cell biology 204, 477–486, doi10.1083/jcb.201311014 (2014).
    OpenUrlAbstract/FREE Full Text
  52. ↵
    Loson, O. C. et al. The mitochondrial fission receptor MiD51 requires ADP as a cofactor. Structure 22, 367–377, doi10.1016/j.str.2014.01.001 (2014).
    OpenUrlCrossRefPubMed
  53. Liu, R. & Chan, D. C. Drp1 recruitment by Mff, MiD51 and MiD49. Molecular biology of the cell 26 (2015).
  54. ↵
    Loson, O. C. et al. Crystal structure and functional analysis of MiD49, a receptor for the mitochondrial fission protein Drp1. Protein Sci 24, 386–394, doi10.1002/pro.2629 (2015).
    OpenUrlCrossRefPubMed
  55. ↵
    Gao, S. et al. Structural basis of oligomerization in the stalk region of dynamin-like MxA. Nature 465, 502–506, doi10.1038/nature08972 (2010).
    OpenUrlCrossRefPubMedWeb of Science
  56. Haller, O., Gao, S., von der Malsburg, A., Daumke, O. & Kochs, G. Dynamin-like MxA GTPase: structural insights into oligomerization and implications for antiviral activity. J Biol Chem 285, 28419–28424, doi10.1074/jbc.R110.145839 (2010).
    OpenUrlAbstract/FREE Full Text
  57. ↵
    Reubold, T. F. et al. Crystal structure of the dynamin tetramer. Nature 525, 404–408, doi10.1038/nature14880 (2015).
    OpenUrlCrossRefPubMed
  58. ↵
    Vanstone, J. R. et al. DNM1L-related mitochondrial fission defect presenting as refractory epilepsy. Eur J Hum Genet 24, 1084–1088, doi10.1038/ejhg.2015.243 (2016).
    OpenUrlCrossRefPubMed
  59. Sheffer, R. et al. Postnatal microcephaly and pain insensitivity due to a de novo heterozygous DNM1L mutation causing impaired mitochondrial fission and function. Am J Med Genet A 170, 1603–1607, doi10.1002/ajmg.a.37624 (2016).
    OpenUrlCrossRefPubMed
  60. ↵
    Chang, C. R. et al. A lethal de novo mutation in the middle domain of the dynamin-related GTPase Drp1 impairs higher order assembly and mitochondrial division. J Biol Chem 285, 32494–32503, doi10.1074/jbc.M110.142430 (2010).
    OpenUrlAbstract/FREE Full Text
  61. ↵
    Gao, S., von der Malsburg, A., Haller, O., Kochs, G. & Daumke, O. Structural basis of oligomerization and the mechano-chemical function in dynamin-like MxA. Faseb Journal 25 (2011).
  62. ↵
    Antonny, B. et al. Membrane fission by dynamin: what we know and what we need to know. Embo J 35, 2270–2284, doi10.15252/embj.201694613 (2016).
    OpenUrlCrossRefPubMed
  63. ↵
    Chappie, J. S. et al. A pseudoatomic model of the dynamin polymer identifies a hydrolysis-dependent powerstroke. Cell 147, 209–222, doi10.1016/j.cell.2011.09.003 (2011).
    OpenUrlCrossRefPubMedWeb of Science
  64. ↵
    Mitchison, T. & Kirschner, M. Dynamic instability of microtubule growth. Nature 312, 237–242 (1984).
    OpenUrlCrossRefPubMedWeb of Science

Extended data References

  1. ↵
    Gibson, D. G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods 6, 343–345, doi10.1038/nmeth.1318 (2009).
    OpenUrlCrossRefPubMedWeb of Science
  2. ↵
    Kalia, R., Talledge, N. & Frost, A. Structural and functional studies of membrane remodeling machines. Methods in cell biology 128, 165–200, doi10.1016/bs.mcb.2015.02.007 (2015).
    OpenUrlCrossRef
  3. ↵
    Blommel, P. G., Becker, K. J., Duvnjak, P. & Fox, B. G. Enhanced Bacterial Protein Expression During Auto-induction Obtained by Alteration of Lac Repressor Dosage and Medium Composition. Biotechnol Prog 23, 585–598, doi10.1021/bp070011x (2007).
    OpenUrlCrossRefPubMed
  4. ↵
    Studier, F. W. Protein production by auto-induction in high density shaking cultures. Protein Expr Purif 41, 207–234 (2005).
    OpenUrlCrossRefPubMedWeb of Science
  5. ↵
    Frohlich, C. et al. Structural insights into oligomerization and mitochondrial remodelling of dynamin 1-like protein. Embo J 32, 1280–1292, doi10.1038/emboj.2013.74 (2013).
    OpenUrlCrossRefPubMed
  6. ↵
    Loson, O. C. et al. Crystal structure and functional analysis of MiD49, a receptor for the mitochondrial fission protein Drp1. Protein Sci 24, 386–394, doi10.1002/pro.2629 (2015).
    OpenUrlCrossRefPubMed
  7. ↵
    Mastronarde, D. N. Automated electron microscope tomography using robust prediction of specimen movements. Journal of structural biology 152, 36–51 (2005).
    OpenUrlCrossRefPubMedWeb of Science
  8. ↵
    Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat Methods 14, 331–332, doi10.1038/nmeth.4193 (2017).
    OpenUrlCrossRefPubMed
  9. ↵
    Zhang, K. Gctf: Real-time CTF determination and correction. Journal of structural biology 193, 1–12, doi10.1016/j.jsb.2015.11.003 (2016).
    OpenUrlCrossRefPubMed
  10. ↵
    Rohou, A. & Grigorieff, N. CTFFIND4: Fast and accurate defocus estimation from electron micrographs. Journal of structural biology 192, 216–221, doi10.1016/j.jsb.2015.08.008 (2015).
    OpenUrlCrossRefPubMed
  11. ↵
    Bell, J. M., Chen, M., Baldwin, P. R. & Ludtke, S. J. High resolution single particle refinement in EMAN2.1. Methods 100, 25–34, doi10.1016/j.ymeth.2016.02.018 (2016).
    OpenUrlCrossRefPubMed
  12. ↵
    Scheres, S. H. W. Semi-automated selection of cryo-EM particles in RELION-1.3. Journal of structural biology 189, 114–122, doi10.1016/j.jsb.2014.11.010 (2015).
    OpenUrlCrossRefPubMed
  13. ↵
    Egelman, E. H. Reconstruction of helical filaments and tubes. Methods Enzymol 482, 167–183, doi10.1016/S0076-6879(10)82006-3 (2010).
    OpenUrlCrossRefPubMedWeb of Science
  14. ↵
    Ge, P. et al. Cryo-EM model of the bullet-shaped vesicular stomatitis virus. Science (New York, N.Y.) 327, 689–693, doi10.1126/science.1181766 (2010).
    OpenUrlAbstract/FREE Full Text
  15. ↵
    Pintilie, G. D., Zhang, J., Goddard, T. D., Chiu, W. & Gossard, D. C. Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions. Journal of structural biology 170, 427–438, doi10.1016/j.jsb.2010.03.007 (2010).
    OpenUrlCrossRefPubMedWeb of Science
  16. Goddard, T. D., Huang, C. C. & Ferrin, T. E. Visualizing density maps with UCSF Chimera. Journal of structural biology 157, 281–287, doi10.1016/j.jsb.2006.06.010 (2007).
    OpenUrlCrossRefPubMedWeb of Science
  17. Goddard, T. D., Huang, C. C. & Ferrin, T. E. Software extensions to UCSF chimera for interactive visualization of large molecular assemblies. Structure 13, 473–482, doi10.1016/j.str.2005.01.006 (2005).
    OpenUrlCrossRefPubMed
  18. Meng, E. C., Pettersen, E. F., Couch, G. S., Huang, C. C. & Ferrin, T. E. Tools for integrated sequence-structure analysis with UCSF Chimera. BMC Bioinformatics 7, 339, doi:10.1186/1471-2105-7-339 (2006).
    OpenUrlCrossRefPubMed
  19. ↵
    Pettersen, E. F. et al. UCSF Chimera‐‐a visualization system for exploratory research and analysis. J Comput Chem 25, 1605–1612, doi10.1002/jcc.20084 (2004).
    OpenUrlCrossRef
  20. ↵
    Wang, R. Y. et al. Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta. eLife 5, doi:10.7554/eLife.17219 (2016).
    OpenUrlCrossRefPubMed
  21. ↵
    Song, Y. et al. High-resolution comparative modeling with RosettaCM. Structure 21, 1735–1742, doi10.1016/j.str.2013.08.005 (2013).
    OpenUrlCrossRefPubMed
  22. ↵
    DiMaio, F., Leaver-Fay, A., Bradley, P., Baker, D. & Andre, I. Modeling symmetric macromolecular structures in Rosetta3. PloS one 6, e20450, doi:10.1371/journal.pone.0020450 (2011).
    OpenUrlCrossRefPubMed
  23. ↵
    DiMaio, F. et al. Atomic-accuracy models from 4.5-A cryo-electron microscopy data with density-guided iterative local refinement. Nature methods 12, 361–365, doi10.1038/nmeth.3286 (2015).
    OpenUrlCrossRefPubMed
  24. ↵
    Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta crystallographica. Section D, Biological crystallography 66, 213221, doi:10.1107/S0907444909052925 (2010).
    OpenUrlCrossRef
  25. ↵
    Kucukelbir, A., Sigworth, F. J. & Tagare, H. D. Quantifying the local resolution of cryo-EM density maps. Nat Methods 11, 63–65, doi10.1038/nmeth.2727 (2014).
    OpenUrlCrossRefPubMedWeb of Science
  26. ↵
    Reubold, T. F. et al. Crystal structure of the dynamin tetramer. Nature 525, 404–408, doi10.1038/nature14880 (2015).
    OpenUrlCrossRefPubMed
Back to top
Posted August 07, 2017.
Download PDF
Email
Structural Basis of Mitochondrial Receptor Binding and GTP-Driven Conformational Constriction by Dynamin-Related Protein 1
Raghav Kalia, Ray Yu-Ruei Wang, Ali Yusuf, Paul V. Thomas, David A. Agard, Janet M. Shaw, Adam Frost
bioRxiv 172809; doi: https://doi.org/10.1101/172809
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools

Subject Area