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- PDB-8qv0: Structure of the native microtubule lattice nucleated from the ye... -

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Basic information

Entry
Database: PDB / ID: 8qv0
TitleStructure of the native microtubule lattice nucleated from the yeast spindle pole body
Components
  • Tubulin alpha-1 chain
  • Tubulin beta chain
KeywordsCELL CYCLE / Microtubule nucleation / MTOC / y-tubulin / SPB
Function / homology
Function and homology information


nuclear migration by microtubule mediated pushing forces / nuclear division / Platelet degranulation / homologous chromosome segregation / nuclear migration along microtubule / tubulin complex / mitotic sister chromatid segregation / nuclear periphery / structural constituent of cytoskeleton / microtubule cytoskeleton organization ...nuclear migration by microtubule mediated pushing forces / nuclear division / Platelet degranulation / homologous chromosome segregation / nuclear migration along microtubule / tubulin complex / mitotic sister chromatid segregation / nuclear periphery / structural constituent of cytoskeleton / microtubule cytoskeleton organization / spindle / mitotic cell cycle / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / hydrolase activity / GTPase activity / GTP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain ...Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
Tubulin beta chain / Tubulin alpha-1 chain
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 6.6 Å
AuthorsDendooven, T. / Yatskevich, S. / Burt, A. / Bellini, D. / Kilmartin, J. / Barford, D.
Funding support United Kingdom, Germany, 3items
OrganizationGrant numberCountry
Cancer Research UK United Kingdom
Boehringer Ingelheim Fonds (BIF) Germany
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Structure of the native γ-tubulin ring complex capping spindle microtubules.
Authors: Tom Dendooven / Stanislau Yatskevich / Alister Burt / Zhuo A Chen / Dom Bellini / Juri Rappsilber / John V Kilmartin / David Barford /
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 ...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.
History
DepositionOct 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulin alpha-1 chain
B: Tubulin beta chain
C: Tubulin alpha-1 chain
D: Tubulin alpha-1 chain
E: Tubulin alpha-1 chain
F: Tubulin alpha-1 chain
G: Tubulin alpha-1 chain
H: Tubulin alpha-1 chain
I: Tubulin alpha-1 chain
J: Tubulin alpha-1 chain
K: Tubulin alpha-1 chain
L: Tubulin alpha-1 chain
M: Tubulin alpha-1 chain
N: Tubulin alpha-1 chain
O: Tubulin beta chain
P: Tubulin beta chain
Q: Tubulin beta chain
R: Tubulin beta chain
S: Tubulin beta chain
T: Tubulin beta chain
U: Tubulin beta chain
V: Tubulin beta chain
W: Tubulin beta chain
X: Tubulin beta chain
Y: Tubulin beta chain
Z: Tubulin beta chain


Theoretical massNumber of molelcules
Total (without water)1,310,67726
Polymers1,310,67726
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Tubulin alpha-1 chain


Mass: 49853.867 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P09733
#2: Protein
Tubulin beta chain


Mass: 50967.457 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PXT5

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: y-Tubulin Ring Complex capping the microtubule minus end
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 6.53
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 4500 nm / Nominal defocus min: 2000 nm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 3 e/Å2 / Avg electron dose per subtomogram: 123 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.17.1_3660: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 130704 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 364 / Num. of volumes extracted: 31720
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003360464
ELECTRON MICROSCOPYf_angle_d0.766488644
ELECTRON MICROSCOPYf_dihedral_angle_d5.78548828
ELECTRON MICROSCOPYf_chiral_restr0.04253248
ELECTRON MICROSCOPYf_plane_restr0.00564584

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