8QV2

Structure of the native y-Tubulin Ring Complex (yTuRC) capping microtubule minus ends at the spindle pole body


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

wwPDB Validation   3D Report Full Report


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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 

  • DOI: https://doi.org/10.1038/s41594-024-01281-y
  • Primary Citation of Related Structures:  
    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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin gamma chain473Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for A0A8H4BZN3 (Saccharomyces cerevisiae)
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UniProt GroupA0A8H4BZN3
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Spindle pole body component823Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for A0A8H4C290 (Saccharomyces cerevisiae)
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Go to UniProtKB:  A0A8H4C290
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UniProt GroupA0A8H4C290
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Spindle pole body component846Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for A0A8H4BVY6 (Saccharomyces cerevisiae)
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UniProt GroupA0A8H4BVY6
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha-1 chain447Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P09733 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP09733
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta chain457Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for A0A6A5PXT5 (Saccharomyces cerevisiae)
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UniProt GroupA0A6A5PXT5
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Spindle pole body component 110944Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for A0A8H8UNQ3 (Saccharomyces cerevisiae)
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UniProt GroupA0A8H8UNQ3
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Unkown protein67Saccharomyces cerevisiaeMutation(s): 0 
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
MC [auth b]
NC [auth c]
OC [auth d]
PC [auth e]
QC [auth f]
MC [auth b],
NC [auth c],
OC [auth d],
PC [auth e],
QC [auth f],
RC [auth g],
SC [auth h],
TC [auth i],
UC [auth j],
VC [auth k],
WC [auth l],
XC [auth m],
YC [auth n]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP
Query on GDP

Download Ideal Coordinates CCD File 
ZC [auth a]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.17.1_3660:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited Kingdom--
Boehringer Ingelheim Fonds (BIF)Germany--
Medical Research Council (MRC, United Kingdom)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-24
    Type: Initial release