User profiles for T. Nakane

Takanori Nakane

Institute of Protein Research, Osaka University
Verified email at protein.osaka-u.ac.jp
Cited by 13162

JSmol and the Next‐Generation Web‐Based Representation of 3D Molecular Structure as Applied to Proteopedia

…, J Prilusky, Z Renjian, T Nakane… - Israel Journal of …, 2013 - Wiley Online Library
… and qualifying as a medical doctor, Nakane decided to enter a four-year … Over the last two
years, Nakane has been developing … Nakane also contributes to several open-source projects, …

New tools for automated high-resolution cryo-EM structure determination in RELION-3

J Zivanov, T Nakane, BO Forsberg, D Kimanius… - elife, 2018 - elifesciences.org
10.7554/eLife.42166.001 Here, we describe the third major release of RELION. CPU-based
vector acceleration has been added in addition to GPU support, which provides flexibility in …

Single-particle cryo-EM at atomic resolution

T Nakane, A Kotecha, A Sente, G McMullan, S Masiulis… - Nature, 2020 - nature.com
The three-dimensional positions of atoms in protein molecules define their structure and their
roles in biological processes. The more precisely atomic coordinates are determined, the …

[HTML][HTML] Structures and distributions of SARS-CoV-2 spike proteins on intact virions

…, J Oton, K Qu, M Cortese, V Zila, L McKeane, T Nakane… - Nature, 2020 - nature.com
T) or nsp3 (Abcam, ab181620; diluted 1:500 in PBS-T). Next, the membranes were washed
3 times in PBS-T… 1 h, washed again 3 times in PBS-T, incubated with western Lightning Plus-…

New tools for automated cryo-EM single-particle analysis in RELION-4.0

D Kimanius, L Dong, G Sharov, T Nakane… - Biochemical …, 2021 - portlandpress.com
… the right shows the value of the supervised threshold (t = T). … the right shows the value of the
supervised threshold (t = T). … on the right shows the value of the supervised threshold (t = T). …

Light-induced structural changes and the site of O= O bond formation in PSII caught by XFEL

…, F Akita, M Sugahara, M Kubo, Y Nakajima, T Nakane… - Nature, 2017 - nature.com
… -I, Continuum) to the sample at t = 0 ms and t = 10 ms (that is, the two flashes were separated
by 10 ms) for the pre-flashed samples, and t = 0 ms and t = 5 ms (separated by 5 ms) for the …

[PDF][PDF] Crystal structure of Cpf1 in complex with guide RNA and target DNA

…, H Hirano, IM Slaymaker, Y Li, I Fedorova, T Nakane… - Cell, 2016 - cell.com
… can explain the requirement of the third T in the 50-TTTN-30 … with the requirement of the
second T in the PAM. The 5-… consistent with the requirement of the first T in the PAM. The K548A …

Structure of the medullary veins of the cerebral hemisphere and related disorders

…, A Fukusumi, T Miyasaka, H Kawai, T Nakane… - Radiographics, 2017 - pubs.rsna.org
Deep medullary veins drain into subependymal veins with four convergence zones and show
parallel distribution patterns adjacent to the body or inferior horn and a radial pattern in the …

A three-dimensional movie of structural changes in bacteriorhodopsin

…, M Kubo, T Nakane, C Wickstrand, T Kimura, T Tanaka… - Science, 2016 - science.org
Bacteriorhodopsin (bR) is a light-driven proton pump and a model membrane transport protein.
We used time-resolved serial femtosecond crystallography at an x-ray free electron laser …

[HTML][HTML] A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis

J Zivanov, T Nakane, SHW Scheres - IUCrJ, 2019 - scripts.iucr.org
A new method to estimate the trajectories of particle motion and the amount of cumulative
beam damage in electron cryo-microscopy (cryo-EM) single-particle analysis is presented. The …