[English] 日本語
Yorodumi
- PDB-9g40: Structure of the Position 7 CMG-decorated gamma-Tubulin Ring Comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9g40
TitleStructure of the Position 7 CMG-decorated gamma-Tubulin Ring Complex from Pig Brain
Components
  • CDK5 regulatory subunit-associated protein 2
  • Gamma-tubulin complex component
  • Gamma-tubulin complex component 3
  • Mitotic-spindle organizing protein 2A isoform X4
KeywordsSTRUCTURAL PROTEIN / Tubulin Complex
Function / homology
Function and homology information


Recruitment of mitotic centrosome proteins and complexes / microtubule organizing center organization / negative regulation of centriole replication / equatorial microtubule organizing center / regulation of mitotic cell cycle spindle assembly checkpoint / microtubule plus-end / polar microtubule / gamma-tubulin complex / microtubule nucleation / microtubule bundle formation ...Recruitment of mitotic centrosome proteins and complexes / microtubule organizing center organization / negative regulation of centriole replication / equatorial microtubule organizing center / regulation of mitotic cell cycle spindle assembly checkpoint / microtubule plus-end / polar microtubule / gamma-tubulin complex / microtubule nucleation / microtubule bundle formation / gamma-tubulin binding / centrosome cycle / Recruitment of NuMA to mitotic centrosomes / 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 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 / positive regulation of microtubule polymerization / centriole / AURKA Activation by TPX2 / tubulin binding / neurogenesis / meiotic cell cycle / chromosome segregation / neuron migration / brain development / spindle / spindle pole / microtubule cytoskeleton organization / Regulation of PLK1 Activity at G2/M Transition / cell junction / mitotic cell cycle / microtubule binding / microtubule / cytoskeleton / transcription cis-regulatory region binding / calmodulin binding / centrosome / protein-containing complex binding / protein kinase binding / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / Golgi apparatus / extracellular exosome / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
CDK5 regulatory subunit-associated protein 2 / 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
Gamma-tubulin complex component / Mitotic-spindle organizing protein 2A isoform X4 / Gamma-tubulin complex component 3 / CDK5 regulatory subunit-associated protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsMunoz-Hernandez, H. / Krutyholowa, R. / Wieczorek, M.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science FoundationTMSGI3_211309 Switzerland
Swiss National Science Foundation310030_208120 Switzerland
CitationJournal: Dev Cell / Year: 2024
Title: Partial closure of the γ-tubulin ring complex by CDK5RAP2 activates microtubule nucleation.
Authors: Yixin Xu / Hugo Muñoz-Hernández / Rościsław Krutyhołowa / Florina Marxer / Ferdane Cetin / Michal Wieczorek /
Abstract: Microtubule nucleation is templated by the γ-tubulin ring complex (γ-TuRC), but its structure deviates from the geometry of α-/β-tubulin in the microtubule, explaining the complex's poor ...Microtubule nucleation is templated by the γ-tubulin ring complex (γ-TuRC), but its structure deviates from the geometry of α-/β-tubulin in the microtubule, explaining the complex's poor nucleating activity. Several proteins may activate the γ-TuRC, but the mechanisms underlying activation are not known. Here, we determined the structure of the porcine γ-TuRC purified using CDK5RAP2's centrosomin motif 1 (CM1). We identified an unexpected conformation of the γ-TuRC bound to multiple protein modules containing MZT2, GCP2, and CDK5RAP2, resulting in a long-range constriction of the γ-tubulin ring that brings it in closer agreement with the 13-protofilament microtubule. Additional CDK5RAP2 promoted γ-TuRC decoration and stimulated the microtubule-nucleating activities of the porcine γ-TuRC and a reconstituted, CM1-free human complex in single-molecule assays. Our results provide a structural mechanism for the control of microtubule nucleation by CM1 proteins and identify conformational transitions in the γ-TuRC that prime it for microtubule nucleation.
History
DepositionJul 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: citation / em_admin / pdbx_entry_details
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
F: Gamma-tubulin complex component 3
G: Gamma-tubulin complex component
X: Mitotic-spindle organizing protein 2A isoform X4
u: CDK5 regulatory subunit-associated protein 2
v: CDK5 regulatory subunit-associated protein 2


Theoretical massNumber of molelcules
Total (without water)652,3915
Polymers652,3915
Non-polymers00
Water00
1


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

-
Components

#1: Protein Gamma-tubulin complex component 3 / Tubulin gamma complex associated protein 3


Mass: 103172.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SsGCP3 / Source: (natural) Sus scrofa (pig) / Organ: brain / References: UniProt: F1RN46
#2: Protein Gamma-tubulin complex component


Mass: 102609.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: brain / References: UniProt: A0A480VJI0
#3: Protein Mitotic-spindle organizing protein 2A isoform X4


Mass: 15920.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: brain / References: UniProt: F1RK97
#4: Protein CDK5 regulatory subunit-associated protein 2 / CDK5 activator-binding protein C48 / Centrosome-associated protein 215


Mass: 215344.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK5RAP2, CEP215, KIAA1633 / Details (production host): (Kan) / Production host: Escherichia coli (E. coli) / Strain (production host): pRARE / References: UniProt: Q96SN8
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Gamma-Tubulin Ring Complex in native pig brain / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionpH: 7.5
Details: Listed in "g-TuRC cryo-EM sample preparation" section.
Buffer component
IDConc.NameBuffer-ID
140 mMHEPES1
2150 mMNaCl1
31 mMMgCl21
41 mMEGTA1
52 mM2-mercaptoethanol1
60.01 % v/vIGEPAL1
70.1 mMGTP1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277.15 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2700 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

CTF correctionType: NONE
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 93207 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00212695
ELECTRON MICROSCOPYf_angle_d0.42917136
ELECTRON MICROSCOPYf_dihedral_angle_d11.6454763
ELECTRON MICROSCOPYf_chiral_restr0.0321914
ELECTRON MICROSCOPYf_plane_restr0.0032188

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more