- EMDB-23639: Single-particle reconstruction of a dimer of the Yeast gamma-TuSC -
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Open data
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Basic information
Entry
Database: EMDB / ID: EMD-23639
Title
Single-particle reconstruction of a dimer of the Yeast gamma-TuSC
Map data
Single-particle reconstruction of a dimer of the Yeast gamma-TuSC half map 1
Sample
Complex: Single-particle reconstruction of a dimer of the Yeast gamma-TuSC
Protein or peptide: Tub4p (gamma-tubulin)
Protein or peptide: Spc97p
Protein or peptide: Spc98p
Function / homology
Function and homology information
gamma-tubulin complex localization to nuclear side of mitotic spindle pole body / protein localization to mitotic spindle pole body / inner plaque of spindle pole body / microtubule nucleation by spindle pole body / outer plaque of spindle pole body / central plaque of spindle pole body / gamma-tubulin small complex / regulation of microtubule nucleation / karyogamy involved in conjugation with cellular fusion / mitotic spindle elongation ...gamma-tubulin complex localization to nuclear side of mitotic spindle pole body / protein localization to mitotic spindle pole body / inner plaque of spindle pole body / microtubule nucleation by spindle pole body / outer plaque of spindle pole body / central plaque of spindle pole body / gamma-tubulin small complex / regulation of microtubule nucleation / karyogamy involved in conjugation with cellular fusion / mitotic spindle elongation / mitotic spindle pole body / equatorial microtubule organizing center / microtubule minus-end binding / gamma-tubulin complex / positive regulation of microtubule nucleation / meiotic spindle organization / microtubule nucleation / positive regulation of cytoplasmic translation / spindle pole body / gamma-tubulin binding / mitotic sister chromatid segregation / spindle assembly / cytoplasmic microtubule organization / mitotic spindle organization / meiotic cell cycle / structural constituent of cytoskeleton / spindle pole / spindle / mitotic cell cycle / protein-containing complex assembly / microtubule / cytoskeleton / calmodulin binding / protein-containing complex binding / GTP binding / nucleus / cytoplasm Similarity search - Function
Spindle pole body component 110 / Spindle pole body component SPC97 / Tubulin gamma chain / Spindle pole body component SPC98 Similarity search - Component
Biological species
Saccharomyces cerevisiae (brewer's yeast)
Method
single particle reconstruction / cryo EM / Resolution: 4.45 Å
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
R01 GM031627
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
R35 GM118099
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
P01 GM105537
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
P41 GM103533
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
GM083960
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
GM109824
United States
National Science Foundation (NSF, United States)
1144247
United States
National Institutes of Health/Office of the Director
1S10OD020054
United States
National Institutes of Health/Office of the Director
1S10OD021741
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
R01 GM124149
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
P30 GM124169
United States
Department of Energy (DOE, United States)
DE-AC02-05CH11231
United States
Citation
Journal: Elife / Year: 2021 Title: CM1-driven assembly and activation of yeast γ-tubulin small complex underlies microtubule nucleation. Authors: Axel F Brilot / Andrew S Lyon / Alex Zelter / Shruthi Viswanath / Alison Maxwell / Michael J MacCoss / Eric G Muller / Andrej Sali / Trisha N Davis / David A Agard / Abstract: Microtubule (MT) nucleation is regulated by the γ-tubulin ring complex (γTuRC), conserved from yeast to humans. In , γTuRC is composed of seven identical γ-tubulin small complex (γTuSC) sub- ...Microtubule (MT) nucleation is regulated by the γ-tubulin ring complex (γTuRC), conserved from yeast to humans. In , γTuRC is composed of seven identical γ-tubulin small complex (γTuSC) sub-assemblies, which associate helically to template MT growth. γTuRC assembly provides a key point of regulation for the MT cytoskeleton. Here, we combine crosslinking mass spectrometry, X-ray crystallography, and cryo-EM structures of both monomeric and dimeric γTuSCs, and open and closed helical γTuRC assemblies in complex with Spc110p to elucidate the mechanisms of γTuRC assembly. γTuRC assembly is substantially aided by the evolutionarily conserved CM1 motif in Spc110p spanning a pair of adjacent γTuSCs. By providing the highest resolution and most complete views of any γTuSC assembly, our structures allow phosphorylation sites to be mapped, surprisingly suggesting that they are mostly inhibitory. A comparison of our structures with the CM1 binding site in the human γTuRC structure at the interface between GCP2 and GCP6 allows for the interpretation of significant structural changes arising from CM1 helix binding to metazoan γTuRC.
History
Deposition
Mar 17, 2021
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Header (metadata) release
May 12, 2021
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Map release
May 12, 2021
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Update
May 19, 2021
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Current status
May 19, 2021
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Specimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
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Image processing
Particle selection
Number selected: 3210917 / Details: cisTEM picking
CTF correction
Software - Name: cisTEM (ver. 1.0 beta) / Details: Final reconstruction in cisTEM
Startup model
Type of model: INSILICO MODEL In silico model: Particle coordinates were semi-automatically picked from filtered and binned images using the e2boxer swarm tool (Tang et al., 2007). Particles were extracted using Relion (Scheres, ...In silico model: Particle coordinates were semi-automatically picked from filtered and binned images using the e2boxer swarm tool (Tang et al., 2007). Particles were extracted using Relion (Scheres, 2012) with a box size of 384 physical pixels resampled to 96 pixels for initial processing. A dataset of ~50,000 particles from 217 micrographs was used to generate 300 2D classes using Relion 1.3. 23 classes were selected and used in the generation of a gamma-TuSC monomer initial model using the e2initialmodel.py function in EMAN2.
Final reconstruction
Number classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1.0 Beta) / Number images used: 506014
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