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- PDB-6x0v: Structure of MZT2/GCP-NHD and CDK5Rap2 at position 13 of the gamm... -

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Entry
Database: PDB / ID: 6x0v
TitleStructure of MZT2/GCP-NHD and CDK5Rap2 at position 13 of the gamma-TuRC
Components
  • Centrosome protein Cep215
  • Gamma-tubulin complex component 2
  • Mitotic-spindle organizing protein 2A
KeywordsSTRUCTURAL 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 / regulation of mitotic cell cycle spindle assembly checkpoint / negative regulation of centriole replication / gamma-tubulin complex / microtubule plus-end / microtubule nucleation / microtubule bundle formation ...gamma-tubulin ring complex => GO:0000931 / ciliary basal body-plasma membrane docking / microtubule organizing center organization / equatorial microtubule organizing center / regulation of mitotic cell cycle spindle assembly checkpoint / negative regulation of centriole replication / 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 / establishment of mitotic spindle orientation / centriole replication / negative regulation of neuron differentiation / spindle assembly / cytoplasmic microtubule / cytoplasmic microtubule organization / positive regulation of microtubule polymerization / 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 / regulation of G2/M transition of mitotic cell cycle / neurogenesis / tubulin binding / AURKA Activation by TPX2 / meiotic cell cycle / chromosome segregation / brain development / neuron migration / spindle / microtubule cytoskeleton organization / spindle pole / G2/M transition of mitotic cell cycle / Regulation of PLK1 Activity at G2/M Transition / mitotic cell cycle / cell junction / microtubule binding / protein-containing complex assembly / microtubule / cytoskeleton / calmodulin binding / transcription cis-regulatory region binding / centrosome / protein kinase binding / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / Golgi apparatus / extracellular exosome / nucleoplasm / membrane / cytosol / cytoplasm
Similarity search - Function
MOZART2 family / Mitotic-spindle organizing gamma-tubulin ring associated / Centrosomin, N-terminal motif 1 / Centrosomin N-terminal motif 1 / 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
Centrosome protein Cep215 / Mitotic-spindle organizing protein 2A / CDK5 regulatory subunit-associated protein 2 / Gamma-tubulin complex component 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsWieczorek, M. / Huang, T.-L. / Urnavicius, L. / Hsia, K.-C. / Kapoor, T.M.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Human Frontier Science Program (HFSP)
Ministry of Science and Technology (MoST, Taiwan)
Academia Sinica (Taiwan)
CitationJournal: 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
DepositionMay 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 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

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Assembly

Deposited unit
E: Mitotic-spindle organizing protein 2A
F: Gamma-tubulin complex component 2
G: Centrosome protein Cep215
H: Centrosome protein Cep215


Theoretical massNumber of molelcules
Total (without water)552,8414
Polymers552,8414
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Mitotic-spindle organizing protein 2A / Mitotic-spindle organizing protein associated with a ring of gamma-tubulin 2A


Mass: 16240.576 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P582
#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
#3: Protein Centrosome protein Cep215 /


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

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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: Focused refinement gamma-TuRC density map surrounding positions 12-13
Type: COMPLEX / Entity ID: all / Source: NATURAL
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 FIELDBright-field microscopy
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: dev_3699: / Classification: refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 137513 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0011326
ELECTRON MICROSCOPYf_angle_d0.3151801
ELECTRON MICROSCOPYf_dihedral_angle_d12.781214
ELECTRON MICROSCOPYf_chiral_restr0.034222
ELECTRON MICROSCOPYf_plane_restr0.001247

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