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Yorodumi- PDB-6v5v: Structure of gamma-tubulin in the native human gamma-tubulin ring... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6v5v | |||||||||
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Title | Structure of gamma-tubulin in the native human gamma-tubulin ring complex | |||||||||
Components | Tubulin gamma-1 chain | |||||||||
Keywords | STRUCTURAL PROTEIN / Tubulin / gamma-tubulin / gamma-tubulin ring complex / gTuRC / g-TuRC / microtubule / microtubule nucleation / single particle cryo-EM structure | |||||||||
Function / homology | Function and homology information mitotic spindle microtubule / polar microtubule / gamma-tubulin complex / meiotic spindle organization / microtubule nucleation / non-motile cilium / pericentriolar material / cytoplasmic microtubule / cell leading edge / mitotic sister chromatid segregation ...mitotic spindle microtubule / polar microtubule / gamma-tubulin complex / meiotic spindle organization / microtubule nucleation / non-motile cilium / pericentriolar material / cytoplasmic microtubule / cell leading edge / mitotic sister chromatid segregation / condensed nuclear chromosome / cytoplasmic microtubule organization / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / centriole / AURKA Activation by TPX2 / mitotic spindle organization / ciliary basal body / recycling endosome / structural constituent of cytoskeleton / microtubule cytoskeleton organization / spindle / Regulation of PLK1 Activity at G2/M Transition / apical part of cell / mitotic cell cycle / microtubule / neuron projection / centrosome / GTP binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Wieczorek, M. / Urnavicius, L. / Ti, S. / Molloy, K.R. / Chait, B.T. / Kapoor, T.M. | |||||||||
Funding support | United States, France, 2items
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Citation | Journal: 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 |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
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PDBx/mmCIF format | 6v5v.cif.gz | 79.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v5v.ent.gz | 57.4 KB | Display | PDB format |
PDBx/mmJSON format | 6v5v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6v5v_validation.pdf.gz | 744.5 KB | Display | wwPDB validaton report |
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Full document | 6v5v_full_validation.pdf.gz | 744.2 KB | Display | |
Data in XML | 6v5v_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 6v5v_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/6v5v ftp://data.pdbj.org/pub/pdb/validation_reports/v5/6v5v | HTTPS FTP |
-Related structure data
Related structure data | 21054MC 6v69C 6v6bC 6v6cC 6v6sC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 51255.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P23258 |
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#2: Chemical | ChemComp-GDP / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Native human gamma-tubulin ring complex / Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 45 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103340 / Symmetry type: POINT | ||||||||||||||||||||||||
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