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- PDB-6v6b: Structures of GCP2 and GCP3 in the native human gamma-tubulin rin... -

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Basic information

Entry
Database: PDB / ID: 6v6b
TitleStructures of GCP2 and GCP3 in the native human gamma-tubulin ring complex
Components
  • Gamma-tubulin complex component 2
  • Gamma-tubulin complex component 3
KeywordsSTRUCTURAL PROTEIN / GCP / GCP2 / GCP3 / gamma-TuSC / gTuSC / gamma-tubulin ring complex / gTuRC / g-TuRC / microtubule / microtubule nucleation / single particle cryo-EM structure
Function / homology
Function and homology information


polar microtubule / gamma-tubulin complex / microtubule nucleation / gamma-tubulin binding / microtubule organizing center / single fertilization / spindle assembly / cytoplasmic microtubule / cytoplasmic microtubule organization / centriole ...polar microtubule / gamma-tubulin complex / microtubule nucleation / gamma-tubulin binding / microtubule organizing center / single fertilization / spindle assembly / cytoplasmic microtubule / cytoplasmic microtubule organization / centriole / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / meiotic cell cycle / brain development / structural constituent of cytoskeleton / spindle / neuron migration / spindle pole / mitotic cell cycle / protein-containing complex assembly / ciliary basal body / centrosome / structural molecule activity / nucleoplasm / membrane / cytoplasm / cytosol
Similarity search - Function
Gamma tubulin complex component, C-terminal / Gamma-tubulin complex component, C-terminal domain superfamily / Gamma tubulin complex component C-terminal / Gamma-tubulin complex component protein / Gamma tubulin complex component protein, N-terminal / Gamma tubulin complex component N-terminal
Similarity search - Domain/homology
Gamma-tubulin complex component 3 / Gamma-tubulin complex component 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsWieczorek, M. / Urnavicius, L. / Ti, S. / Molloy, K.R. / Chait, B.T. / Kapoor, T.M.
Funding support United States, France, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM130234 United States
Human Frontier Science Program (HFSP)LT000025/18-L1 France
CitationJournal: Cell / Year: 2020
Title: Asymmetric Molecular Architecture of the Human γ-Tubulin Ring Complex.
Authors: Michal Wieczorek / Linas Urnavicius / Shih-Chieh Ti / Kelly R Molloy / Brian T Chait / Tarun M Kapoor /
Abstract: The γ-tubulin ring complex (γ-TuRC) is an essential regulator of centrosomal and acentrosomal microtubule formation, yet its structure is not known. Here, we present a cryo-EM reconstruction of the ...The γ-tubulin ring complex (γ-TuRC) is an essential regulator of centrosomal and acentrosomal microtubule formation, yet its structure is not known. Here, we present a cryo-EM reconstruction of the native human γ-TuRC at ∼3.8 Å resolution, revealing an asymmetric, cone-shaped structure. Pseudo-atomic models indicate that GCP4, GCP5, and GCP6 form distinct Y-shaped assemblies that structurally mimic GCP2/GCP3 subcomplexes distal to the γ-TuRC "seam." We also identify an unanticipated structural bridge that includes an actin-like protein and spans the γ-TuRC lumen. Despite its asymmetric architecture, the γ-TuRC arranges γ-tubulins into a helical geometry poised to nucleate microtubules. Diversity in the γ-TuRC subunits introduces large (>100,000 Å) surfaces in the complex that allow for interactions with different regulatory factors. The observed compositional complexity of the γ-TuRC could self-regulate its assembly into a cone-shaped structure to control microtubule formation across diverse contexts, e.g., within biological condensates or alongside existing filaments.
History
DepositionDec 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.0Jan 1, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 1, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.0Jan 1, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 1, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 1, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jan 1, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 1, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 1, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3May 28, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 28, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Assembly

Deposited unit
B: Gamma-tubulin complex component 3
C: Gamma-tubulin complex component 2


Theoretical massNumber of molelcules
Total (without water)209,4762
Polymers209,4762
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Gamma-tubulin complex component 3 / hGCP3 / Gamma-ring complex protein 104 kDa / hGrip104 / Spindle pole body protein Spc98 homolog / hSpc98


Mass: 103710.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96CW5
#2: Protein Gamma-tubulin complex component 2 / hGCP2 / Gamma-ring complex protein 103 kDa / hGrip103 / Spindle pole body protein Spc97 homolog / hSpc97


Mass: 105765.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BSJ2
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Native human gamma-tubulin ring complex / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
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: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 351714 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0059300
ELECTRON MICROSCOPYf_angle_d0.51812542
ELECTRON MICROSCOPYf_dihedral_angle_d11.0545582
ELECTRON MICROSCOPYf_chiral_restr0.0411405
ELECTRON MICROSCOPYf_plane_restr0.0041576

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