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Yorodumi- PDB-6x0v: Structure of MZT2/GCP-NHD and CDK5Rap2 at position 13 of the gamm... -
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-Basic information
Entry | Database: PDB / ID: 6x0v | |||||||||||||||
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Title | Structure of MZT2/GCP-NHD and CDK5Rap2 at position 13 of the gamma-TuRC | |||||||||||||||
Components |
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Keywords | STRUCTURAL PROTEIN / gamma-TuRC / MZT2 / GCP / CDK5Rap2 | |||||||||||||||
Function / homology | Function and homology information gamma-tubulin ring complex => GO:0000931 / ciliary basal body-plasma membrane docking / microtubule organizing center organization / equatorial microtubule organizing center / negative regulation of centriole replication / regulation of mitotic cell cycle spindle assembly checkpoint / microtubule minus-end binding / gamma-tubulin complex / microtubule plus-end / microtubule nucleation ...gamma-tubulin ring complex => GO:0000931 / ciliary basal body-plasma membrane docking / microtubule organizing center organization / equatorial microtubule organizing center / negative regulation of centriole replication / regulation of mitotic cell cycle spindle assembly checkpoint / microtubule minus-end binding / gamma-tubulin complex / microtubule plus-end / microtubule nucleation / microtubule bundle formation / gamma-tubulin binding / centrosome cycle / microtubule organizing center / regulation of neuron differentiation / pericentriolar material / mitotic spindle pole / cytoplasmic microtubule / establishment of mitotic spindle orientation / centriole replication / negative regulation of neuron differentiation / spindle assembly / 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 / positive regulation of microtubule polymerization / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / regulation of G2/M transition of mitotic cell cycle / tubulin binding / AURKA Activation by TPX2 / neurogenesis / meiotic cell cycle / chromosome segregation / neuron migration / brain development / spindle pole / microtubule cytoskeleton organization / spindle / G2/M transition of mitotic cell cycle / Regulation of PLK1 Activity at G2/M Transition / cell junction / mitotic cell cycle / microtubule binding / protein-containing complex assembly / microtubule / cytoskeleton / calmodulin binding / transcription cis-regulatory region binding / centrosome / protein kinase binding / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / Golgi apparatus / extracellular exosome / nucleoplasm / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||||||||
Authors | Wieczorek, M. / Huang, T.-L. / Urnavicius, L. / Hsia, K.-C. / Kapoor, T.M. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Cell Rep / Year: 2020 Title: MZT Proteins Form Multi-Faceted Structural Modules in the γ-Tubulin Ring Complex. Authors: Michal Wieczorek / Tzu-Lun Huang / Linas Urnavicius / Kuo-Chiang Hsia / Tarun M Kapoor / Abstract: Microtubule organization depends on the γ-tubulin ring complex (γ-TuRC), a ∼2.3-MDa nucleation factor comprising an asymmetric assembly of γ-tubulin and GCP2-GCP6. However, it is currently ...Microtubule organization depends on the γ-tubulin ring complex (γ-TuRC), a ∼2.3-MDa nucleation factor comprising an asymmetric assembly of γ-tubulin and GCP2-GCP6. However, it is currently unclear how the γ-TuRC-associated microproteins MZT1 and MZT2 contribute to the structure and regulation of the holocomplex. Here, we report cryo-EM structures of MZT1 and MZT2 in the context of the native human γ-TuRC. MZT1 forms two subcomplexes with the N-terminal α-helical domains of GCP3 or GCP6 (GCP-NHDs) within the γ-TuRC "lumenal bridge." We determine the X-ray structure of recombinant MZT1/GCP6-NHD and find it is similar to that within the native γ-TuRC. We identify two additional MZT/GCP-NHD-like subcomplexes, one of which is located on the outer face of the γ-TuRC and comprises MZT2 and GCP2-NHD in complex with a centrosomin motif 1 (CM1)-containing peptide. Our data reveal how MZT1 and MZT2 establish multi-faceted, structurally mimetic "modules" that can expand structural and regulatory interfaces in the γ-TuRC. | |||||||||||||||
History |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 6x0v.cif.gz | 133.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6x0v.ent.gz | 48.5 KB | Display | PDB format |
PDBx/mmJSON format | 6x0v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6x0v_validation.pdf.gz | 1013.9 KB | Display | wwPDB validaton report |
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Full document | 6x0v_full_validation.pdf.gz | 1015.2 KB | Display | |
Data in XML | 6x0v_validation.xml.gz | 14 KB | Display | |
Data in CIF | 6x0v_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x0/6x0v ftp://data.pdbj.org/pub/pdb/validation_reports/x0/6x0v | HTTPS FTP |
-Related structure data
Related structure data | 21985MC 6m33C 6x0uC 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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-Components
#1: Protein | Mass: 16240.576 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P582 |
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#2: Protein | Mass: 105765.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BSJ2 |
#3: Protein | Mass: 215417.359 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q66GT8, UniProt: Q96SN8*PLUS |
-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: Focused refinement gamma-TuRC density map surrounding positions 12-13 Type: COMPLEX / Entity ID: all / Source: NATURAL |
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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 K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: dev_3699: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 137513 / Symmetry type: POINT | ||||||||||||||||||||||||
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