[English] 日本語
Yorodumi
- PDB-6v6s: Structure of the native human gamma-tubulin ring complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6v6s
TitleStructure of the native human gamma-tubulin ring complex
Components
  • (Gamma-tubulin complex component ...) x 5
  • (Unassigned poly-alanine model ...) x 3
  • Tubulin gamma-1 chain
  • Unassigned poly-alanine chain ("staple")
  • beta actin
KeywordsSTRUCTURAL PROTEIN / Tubulin / gamma-tubulin / gamma-tubulin ring complex / gTuRC / g-TuRC / GCP / GCP2 / GCP3 / GCP4 / GCP5 / GCP6 / microtubule / microtubule nucleation / single particle cryo-EM structure
Function / homology
Function and homology information


equatorial microtubule organizing center / mitotic spindle microtubule / gamma-tubulin ring complex / polar microtubule / gamma-tubulin complex / meiotic spindle organization / microtubule nucleation / non-motile cilium / gamma-tubulin binding / microtubule organizing center ...equatorial microtubule organizing center / mitotic spindle microtubule / gamma-tubulin ring complex / polar microtubule / gamma-tubulin complex / meiotic spindle organization / microtubule nucleation / non-motile cilium / gamma-tubulin binding / microtubule organizing center / pericentriolar material / single fertilization / cell leading edge / mitotic sister chromatid segregation / spindle assembly / cytoplasmic microtubule / 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 / meiotic cell cycle / condensed nuclear chromosome / brain development / neuron migration / structural constituent of cytoskeleton / spindle / microtubule cytoskeleton organization / recycling endosome / spindle pole / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / apical part of cell / mitotic cell cycle / microtubule binding / protein-containing complex assembly / microtubule / neuron projection / centrosome / GTP binding / structural molecule activity / nucleoplasm / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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 ...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
ADENOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-DIPHOSPHATE / Tubulin gamma-1 chain / Gamma-tubulin complex component 3 / Gamma-tubulin complex component 6 / Gamma-tubulin complex component 5 / Gamma-tubulin complex component 2 / Gamma-tubulin complex component 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsWieczorek, M. / Urnavicius, L. / Ti, S. / Molloy, K.R. / Chait, B.T. / Kapoor, T.M.
Funding support United States, France, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM130234 United States
Human Frontier Science Program (HFSP)LT000025/18-L1 France
CitationJournal: 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
DepositionDec 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Mar 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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-21073
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gamma-tubulin complex component 2
B: Gamma-tubulin complex component 3
C: Gamma-tubulin complex component 2
D: Gamma-tubulin complex component 3
E: Gamma-tubulin complex component 2
F: Gamma-tubulin complex component 3
G: Gamma-tubulin complex component 2
H: Gamma-tubulin complex component 3
I: Gamma-tubulin complex component 4
J: Gamma-tubulin complex component 5
K: Gamma-tubulin complex component 4
L: Gamma-tubulin complex component 6
M: Gamma-tubulin complex component 2
N: Unassigned poly-alanine chain ("staple")
O: Unassigned poly-alanine chain ("staple")
Q: Unassigned poly-alanine chain ("staple")
R: Unassigned poly-alanine chain ("staple")
S: Unassigned poly-alanine chain ("staple")
T: Gamma-tubulin complex component 3
U: beta actin
V: Unassigned poly-alanine model ("CC")
W: Unassigned poly-alanine model ("HB")
X: Unassigned poly-alanine model ("Lumenal bridge helical bundles")
Y: Unassigned poly-alanine model ("CC")
a: Tubulin gamma-1 chain
b: Tubulin gamma-1 chain
c: Tubulin gamma-1 chain
d: Tubulin gamma-1 chain
e: Tubulin gamma-1 chain
f: Tubulin gamma-1 chain
g: Tubulin gamma-1 chain
h: Tubulin gamma-1 chain
i: Tubulin gamma-1 chain
j: Tubulin gamma-1 chain
k: Tubulin gamma-1 chain
l: Tubulin gamma-1 chain
m: Tubulin gamma-1 chain
t: Tubulin gamma-1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,353,97453
Polymers2,347,34238
Non-polymers6,63215
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Gamma-tubulin complex component ... , 5 types, 14 molecules ACEGMBDFHTIKJL

#1: 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.: 5 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BSJ2
#2: Protein
Gamma-tubulin complex component 3 / hGCP3 / Gamma-ring complex protein 104 kDa / hGrip104 / Spindle pole body protein Spc98 homolog / hSpc98


Mass: 103710.102 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96CW5
#3: Protein Gamma-tubulin complex component 4 / hGCP4 / Gamma-ring complex protein 76 kDa / hGrip76


Mass: 76179.969 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UGJ1
#4: Protein Gamma-tubulin complex component 5 / GCP-5


Mass: 118467.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96RT8
#5: Protein Gamma-tubulin complex component 6 / GCP-6


Mass: 200733.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Sequence truncated around modeled region of GCP6 to enable deposition; full sequence can be found at Uniprot # Q96RT7.
Source: (natural) Homo sapiens (human) / References: UniProt: Q96RT7

-
Protein/peptide , 1 types, 5 molecules NOQRS

#6: Protein/peptide
Unassigned poly-alanine chain ("staple")


Mass: 4273.259 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

-
Protein , 2 types, 15 molecules Uabcdefghijklmt

#7: Protein beta actin


Mass: 41723.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#11: Protein
Tubulin gamma-1 chain / Gamma-1-tubulin / Gamma-tubulin complex component 1 / GCP-1


Mass: 51255.824 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P23258

-
Unassigned poly-alanine model ... , 3 types, 4 molecules VYWX

#8: Protein Unassigned poly-alanine model ("CC")


Mass: 5634.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#9: Protein Unassigned poly-alanine model ("HB")


Mass: 14060.317 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#10: Protein Unassigned poly-alanine model ("Lumenal bridge helical bundles")


Mass: 22400.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

-
Non-polymers , 2 types, 15 molecules

#12: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#13: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Native human gamma-tubulin ring complex / Type: COMPLEX / Entity ID: #1-#6, #8-#10 / 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

-
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 K2 SUMMIT (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103172 / Symmetry type: POINT

+
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