[English] 日本語
Yorodumi
- PDB-9g3z: Structure of the Open gamma-Tubulin Ring Complex from Pig Brain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9g3z
TitleStructure of the Open gamma-Tubulin Ring Complex from Pig Brain
Components
  • (Gamma-tubulin complex ...) x 4
  • (Tubulin gamma ...) x 2
  • CDK5 regulatory subunit-associated protein 2
  • Mitotic spindle organizing protein 1
  • Mitotic-spindle organizing protein 2A isoform X4
KeywordsSTRUCTURAL PROTEIN / Tubulin Complex
Function / homology
Function and homology information


microtubule minus-end binding / microtubule nucleation by interphase microtubule organizing center / gamma-tubulin complex localization / Recruitment of mitotic centrosome proteins and complexes / equatorial microtubule organizing center / gamma-tubulin ring complex / interphase microtubule organizing center / polar microtubule / gamma-tubulin complex / microtubule nucleation ...microtubule minus-end binding / microtubule nucleation by interphase microtubule organizing center / gamma-tubulin complex localization / Recruitment of mitotic centrosome proteins and complexes / equatorial microtubule organizing center / gamma-tubulin ring complex / interphase microtubule organizing center / polar microtubule / gamma-tubulin complex / microtubule nucleation / gamma-tubulin binding / Recruitment of NuMA to mitotic centrosomes / pericentriolar material / cytoplasmic microtubule / mitotic spindle assembly / spindle assembly / cytoplasmic microtubule organization / centriole / meiotic cell cycle / spindle microtubule / neuron migration / brain development / microtubule cytoskeleton organization / spindle pole / spindle / cell junction / mitotic cell cycle / microtubule binding / microtubule / calmodulin binding / centrosome / GTP binding / nucleoplasm / 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 / Mitotic-spindle organizing protein 1 / Mitotic-spindle organizing gamma-tubulin ring associated / Gamma-tubulin complex component 6, N-terminal / Gamma-tubulin complex component 6 N-terminus / Gamma tubulin ...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 / Mitotic-spindle organizing protein 1 / Mitotic-spindle organizing gamma-tubulin ring associated / Gamma-tubulin complex component 6, N-terminal / Gamma-tubulin complex component 6 N-terminus / Gamma tubulin / 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 / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
CDK5 regulatory subunit-associated protein 2 / Gamma-tubulin complex component / Tubulin gamma chain / Mitotic spindle organizing protein 1 / Gamma-tubulin complex component / Gamma-tubulin complex component / Tubulin gamma complex component 6 / Mitotic-spindle organizing protein 2A isoform X4 / Gamma-tubulin complex component 3
Similarity search - Component
Biological speciesSus scrofa (pig)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsMunoz-Hernandez, H. / 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
O: Mitotic spindle organizing protein 1
P: Mitotic spindle organizing protein 1
Q: Mitotic spindle organizing protein 1
Y: Mitotic-spindle organizing protein 2A isoform X4
a: Tubulin gamma chain
m: Tubulin gamma chain
w: CDK5 regulatory subunit-associated protein 2
x: CDK5 regulatory subunit-associated protein 2
N: Gamma-tubulin complex component 3
M: Gamma-tubulin complex component
L: Tubulin gamma complex associated protein 6
A: Gamma-tubulin complex component
B: Gamma-tubulin complex component 3
C: Gamma-tubulin complex component
H: Gamma-tubulin complex component 3
D: Gamma-tubulin complex component 3
E: Gamma-tubulin complex component
F: Gamma-tubulin complex component 3
G: Gamma-tubulin complex component
I: Gamma-tubulin complex component
b: Tubulin gamma chain
c: Tubulin gamma chain
d: Tubulin gamma chain
e: Tubulin gamma chain
f: Tubulin gamma chain
g: Tubulin gamma chain
h: Tubulin gamma chain
i: Tubulin gamma chain
n: Tubulin gamma chain
K: Gamma-tubulin complex component
J: Gamma-tubulin complex component
k: Tubulin gamma chain
j: Tubulin gamma chain
l: Tubulin gamma chain


Theoretical massNumber of molelcules
Total (without water)2,626,34234
Polymers2,626,34234
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein , 3 types, 6 molecules OPQYwx

#1: Protein Mitotic spindle organizing protein 1


Mass: 8285.489 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: MZT1 / Production host: Sus scrofa (pig) / References: UniProt: A0A4X1VBW8
#2: Protein Mitotic-spindle organizing protein 2A isoform X4


Mass: 15920.321 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: LOC100153925 / Production host: Sus scrofa (pig) / References: UniProt: F1RK97
#4: Protein CDK5 regulatory subunit-associated protein 2


Mass: 189905.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Human sequence used for CDK5RAP251-100 / Source: (gene. exp.) Homo sapiens (human) / Gene: CDK5RAP2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A0MRG9

-
Tubulin gamma ... , 2 types, 15 molecules ambcdefghinkjlL

#3: Protein
Tubulin gamma chain


Mass: 51135.562 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: TUBG2 / Production host: Sus scrofa (pig) / References: UniProt: A0A287BRH5
#7: Protein Tubulin gamma complex associated protein 6


Mass: 188644.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: TUBGCP6 / Production host: Sus scrofa (pig) / References: UniProt: A0A8W4FDV6

-
Gamma-tubulin complex ... , 4 types, 13 molecules NBHDFMACEGIKJ

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


Mass: 103172.477 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: TUBGCP3 / Production host: Sus scrofa (pig) / References: UniProt: F1RN46
#6: Protein
Gamma-tubulin complex component


Mass: 102609.703 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Sus scrofa (pig) / References: UniProt: A0A8D1IGH3
#8: Protein Gamma-tubulin complex component


Mass: 76104.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: TUBGCP4 / Production host: Sus scrofa (pig) / References: UniProt: A0A8D1V2H0
#9: Protein Gamma-tubulin complex component


Mass: 120090.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Sus scrofa (pig) / References: UniProt: A0A287B1K1

-
Details

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 from native pig brain / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE-PROPANE

-
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: 2900 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: 80608 / Symmetry type: POINT
Atomic model buildingProtocol: BACKBONE TRACE / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 247.43 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002478226
ELECTRON MICROSCOPYf_angle_d0.5901108889
ELECTRON MICROSCOPYf_chiral_restr0.039115056
ELECTRON MICROSCOPYf_plane_restr0.004215713
ELECTRON MICROSCOPYf_dihedral_angle_d5.273115713

+
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://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