[English] 日本語
Yorodumi
- PDB-7m2y: Closed conformation of the Yeast wild-type gamma-TuRC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7m2y
TitleClosed conformation of the Yeast wild-type gamma-TuRC
Components
  • Spindle pole body component 110
  • Spindle pole body component SPC97
  • Spindle pole body component SPC98
  • Tubulin gamma chain
KeywordsCELL CYCLE / microtubule nucleation
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 / microtubule nucleation by spindle pole body / gamma-tubulin small complex => GO:0008275 / inner plaque of spindle pole body / outer plaque of spindle pole body / central plaque of spindle pole body / gamma-tubulin small complex / equatorial microtubule organizing center / karyogamy involved in conjugation with cellular fusion ...gamma-tubulin complex localization to nuclear side of mitotic spindle pole body / protein localization to mitotic spindle pole body / microtubule nucleation by spindle pole body / gamma-tubulin small complex => GO:0008275 / inner plaque of spindle pole body / outer plaque of spindle pole body / central plaque of spindle pole body / gamma-tubulin small complex / equatorial microtubule organizing center / karyogamy involved in conjugation with cellular fusion / mitotic spindle pole body / mitotic spindle elongation / gamma-tubulin complex / meiotic spindle organization / positive regulation of cytoplasmic translation / microtubule nucleation / positive regulation of microtubule nucleation / gamma-tubulin binding / spindle pole body / mitotic sister chromatid segregation / cytoplasmic microtubule organization / spindle assembly / meiotic cell cycle / microtubule cytoskeleton organization / structural constituent of cytoskeleton / mitotic spindle organization / spindle / spindle pole / mitotic cell cycle / protein-containing complex assembly / microtubule / calmodulin binding / GTPase activity / GTP binding / protein-containing complex binding / nucleus / cytoplasm
Similarity search - Function
Spindle pole body component 110, C-terminal / Spindle pole body component 110 C-terminal domain / Gamma tubulin / Gamma-tubulin complex, C-terminal domain superfamily / Gamma-tubulin complex component protein / Gamma tubulin complex component, C-terminal / Gamma tubulin complex component protein, N-terminal / Gamma tubulin complex component C-terminal / Gamma tubulin complex component N-terminal / Tubulin, C-terminal ...Spindle pole body component 110, C-terminal / Spindle pole body component 110 C-terminal domain / Gamma tubulin / Gamma-tubulin complex, C-terminal domain superfamily / Gamma-tubulin complex component protein / Gamma tubulin complex component, C-terminal / Gamma tubulin complex component protein, N-terminal / Gamma tubulin complex component C-terminal / Gamma tubulin complex component N-terminal / Tubulin, C-terminal / Tubulin / Tubulin C-terminal domain / Tubulin subunits alpha, beta, and gamma signature. / Tubulin, conserved site / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
Tubulin gamma chain / GUANOSINE-5'-DIPHOSPHATE / Spindle pole body component SPC97 / Spindle pole body component 110 / Spindle pole body component SPC98
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.03 Å
AuthorsBrilot, A.F. / Lyon, A.S. / Zelter, A. / Viswanath, S. / Maxwell, A. / MacCoss, M.J. / Muller, E.G. / Sali, A. / Davis, T.N. / Agard, D.A.
Funding support United States, 13items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)David Agard United States
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 Director1S10OD020054 United States
National Institutes of Health/Office of the Director1S10OD021741 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
CitationJournal: 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
DepositionMar 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-23637
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-23637
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tubulin gamma chain
B: Tubulin gamma chain
C: Spindle pole body component SPC98
D: Spindle pole body component SPC97
U: Spindle pole body component 110
hetero molecules


Theoretical massNumber of molelcules
Total (without water)326,9557
Polymers326,0695
Non-polymers8862
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area21090 Å2
ΔGint-91 kcal/mol
Surface area95180 Å2

-
Components

#1: Protein Tubulin gamma chain / Gamma-tubulin


Mass: 52671.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: TUB4, YLR212C, L8167.21 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P53378
#2: Protein Spindle pole body component SPC98 /


Mass: 98336.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SPC98, YNL126W, N1222, N1879 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P53540
#3: Protein Spindle pole body component SPC97 /


Mass: 96940.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SPC97, YHR172W / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P38863
#4: Protein Spindle pole body component 110 / / Extragenic suppressor of CMD1-1 mutant protein 1 / Nuclear filament-related protein 1 / Spindle ...Extragenic suppressor of CMD1-1 mutant protein 1 / Nuclear filament-related protein 1 / Spindle pole body spacer protein SPC110


Mass: 25449.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SPC110, NUF1, XCM1, YDR356W, D9476.3 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P32380
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

-
Sample preparation

ComponentName: Closed conformation of the Yeast wild-type gamma-TuRC / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightUnits: MEGADALTONS / Experimental value: YES
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast) / Cellular location: Spindle Pole Body / Organelle: Nucleus
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Strain: SF9
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
140 mMHEPES-KOH1
2100 mMPotassium Chloride1
32 mMMagnesium Chloride1
41 mMEGTA1
51 mMGDP1
62.5 %v/vGlycerol1
71 mMDTT1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K / Details: Whatman #1 Filter papers used.

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 47214 X / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 15 sec. / Electron dose: 80 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1
Image scansMovie frames/image: 75

-
Processing

EM software
IDNameVersionCategoryDetails
2SerialEMimage acquisition
4cisTEM1.0 betaCTF correction
7PHENIXmodel fitting
8Cootmodel fitting
9Rosettamodel fitting
11RELION2.1initial Euler assignment
12cisTEM1.0 Betafinal Euler assignment
13cisTEM1.0 BetaclassificationFocused classification
14cisTEM1.0 Beta3D reconstruction
15PHENIXmodel refinement
16Cootmodel refinement
17Rosettamodel refinement
CTF correctionDetails: Final reconstruction in cisTEM / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 0 ° / Axial rise/subunit: 0.01 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 28753
Details: Boxed approximately every 3 asymmetric units using a rise of 21 Angstroms, with a box size of 600 physical pixels (635.4A).
3D reconstructionResolution: 4.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20420 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL
Atomic model buildingB value: 130 / Protocol: OTHER / Space: REAL

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • New page: Covid-19 featured information page in EM Navigator

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB at PDBe / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more