8QRY | pdb_00008qry

Crystal structure of the yeast spindle body component Spc98


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 
    0.302 (Depositor), 0.319 (DCC) 
  • R-Value Work: 
    0.238 (Depositor), 0.246 (DCC) 
  • R-Value Observed: 
    0.241 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Structure of the native gamma-tubulin ring complex capping spindle microtubules.

Dendooven, T.Yatskevich, S.Burt, A.Chen, Z.A.Bellini, D.Rappsilber, J.Kilmartin, J.V.Barford, D.

(2024) Nat Struct Mol Biol 31: 1134-1144

  • DOI: https://doi.org/10.1038/s41594-024-01281-y
  • Primary Citation Related Structures: 
    8QRY, 8QV0, 8QV2, 8QV3

  • PubMed Abstract: 

    Microtubule (MT) filaments, composed of α/β-tubulin dimers, are fundamental to cellular architecture, function and organismal development. They are nucleated from MT organizing centers by the evolutionarily conserved γ-tubulin ring complex (γTuRC). However, the molecular mechanism of nucleation remains elusive. Here we used cryo-electron tomography to determine the structure of the native γTuRC capping the minus end of a MT in the context of enriched budding yeast spindles. In our structure, γTuRC presents a ring of γ-tubulin subunits to seed nucleation of exclusively 13-protofilament MTs, adopting an active closed conformation to function as a perfect geometric template for MT nucleation. Our cryo-electron tomography reconstruction revealed that a coiled-coil protein staples the first row of α/β-tubulin of the MT to alternating positions along the γ-tubulin ring of γTuRC. This positioning of α/β-tubulin onto γTuRC suggests a role for the coiled-coil protein in augmenting γTuRC-mediated MT nucleation. Based on our results, we describe a molecular model for budding yeast γTuRC activation and MT nucleation.


  • Organizational Affiliation
    • MRC Laboratory of Molecular Biology, Cambridge, UK. tdendooven@mrc-lmb.cam.ac.uk.

Macromolecule Content 

  • Total Structure Weight: 10.83 kDa 
  • Atom Count: 806 
  • Modeled Residue Count: 96 
  • Deposited Residue Count: 96 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Spindle pole body component96Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SPC98
UniProt
Find proteins for P53540 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53540 
Go to UniProtKB:  P53540
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53540
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free:  0.302 (Depositor), 0.319 (DCC) 
  • R-Value Work:  0.238 (Depositor), 0.246 (DCC) 
  • R-Value Observed: 0.241 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 28.304α = 90
b = 45.284β = 90
c = 65.569γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
MOLREPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-03
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Database references, Structure summary