[English] 日本語
Yorodumi
- PDB-7as4: Recombinant human gTuRC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7as4
TitleRecombinant human gTuRC
Components
  • (Gamma-tubulin complex component ...) x 5
  • Actin, cytoplasmic 1
  • Mitotic-spindle organizing protein 1
  • Tubulin gamma-1 chain
KeywordsCELL CYCLE / microtubule organizing center / microtubule / gamma-tubulin ring complex / gamma-tubulin small complex / spindle organization / microtubule nucleation
Function / homology
Function and homology information


microtubule nucleation by interphase microtubule organizing center / gamma-tubulin complex localization / microtubule nucleator activity / positive regulation of norepinephrine uptake / polar microtubule / interphase microtubule organizing center / gamma-tubulin complex / gamma-tubulin ring complex / mitotic spindle microtubule / Formation of the embryonic stem cell BAF (esBAF) complex ...microtubule nucleation by interphase microtubule organizing center / gamma-tubulin complex localization / microtubule nucleator activity / positive regulation of norepinephrine uptake / polar microtubule / interphase microtubule organizing center / gamma-tubulin complex / gamma-tubulin ring complex / mitotic spindle microtubule / Formation of the embryonic stem cell BAF (esBAF) complex / bBAF complex / cellular response to cytochalasin B / meiotic spindle organization / npBAF complex / brahma complex / nBAF complex / Formation of the canonical BAF (cBAF) complex / regulation of transepithelial transport / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / Formation of the polybromo-BAF (pBAF) complex / morphogenesis of a polarized epithelium / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / structural constituent of postsynaptic actin cytoskeleton / Formation of the non-canonical BAF (ncBAF) complex / Gap junction degradation / microtubule nucleation / GBAF complex / Cell-extracellular matrix interactions / regulation of G0 to G1 transition / protein localization to adherens junction / dense body / Folding of actin by CCT/TriC / Tat protein binding / postsynaptic actin cytoskeleton / RSC-type complex / gamma-tubulin binding / Regulation of CDH1 Function / regulation of double-strand break repair / regulation of nucleotide-excision repair / Prefoldin mediated transfer of substrate to CCT/TriC / non-motile cilium / Adherens junctions interactions / RHOF GTPase cycle / adherens junction assembly / apical protein localization / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / tight junction / Sensory processing of sound by inner hair cells of the cochlea / positive regulation of T cell differentiation / apical junction complex / positive regulation of double-strand break repair / regulation of norepinephrine uptake / transporter regulator activity / maintenance of blood-brain barrier / ciliary transition zone / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / pericentriolar material / establishment or maintenance of cell polarity / cell leading edge / Regulation of MITF-M-dependent genes involved in pigmentation / cortical cytoskeleton / Recycling pathway of L1 / mitotic sister chromatid segregation / microtubule organizing center / nitric-oxide synthase binding / regulation of G1/S transition of mitotic cell cycle / brush border / EPH-ephrin mediated repulsion of cells / mitotic spindle assembly / negative regulation of cell differentiation / RHO GTPases Activate WASPs and WAVEs / regulation of synaptic vesicle endocytosis / positive regulation of myoblast differentiation / kinesin binding / single fertilization / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / positive regulation of double-strand break repair via homologous recombination / cytoplasmic microtubule / spindle assembly / cytoplasmic microtubule organization / EPHB-mediated forward signaling / cytoskeleton 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 / axonogenesis / substantia nigra development / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / calyx of Held / AURKA Activation by TPX2 / nitric-oxide synthase regulator activity / mitotic spindle organization / condensed nuclear chromosome
Similarity search - Function
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 ...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 / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Actin / Actin family / Actin / 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 / ATPase, nucleotide binding domain
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Tubulin gamma-1 chain / Actin, cytoplasmic 1 / Mitotic-spindle organizing protein 1 / 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: 4.13 Å
AuthorsSerna, M. / Fernandez-Leiro, R. / Llorca, O.
Funding support Spain, 3items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesSAF2017-82632-P Spain
Other governmentY2018/BIO4747 Spain
Other governmentP2018/NMT4443 Spain
CitationJournal: Sci Adv / Year: 2020
Title: Assembly of the asymmetric human γ-tubulin ring complex by RUVBL1-RUVBL2 AAA ATPase.
Authors: Fabian Zimmermann / Marina Serna / Artur Ezquerra / Rafael Fernandez-Leiro / Oscar Llorca / Jens Luders /
Abstract: The microtubule nucleator γ-tubulin ring complex (γTuRC) is essential for the function of microtubule organizing centers such as the centrosome. Since its discovery over two decades ago, γTuRC has ...The microtubule nucleator γ-tubulin ring complex (γTuRC) is essential for the function of microtubule organizing centers such as the centrosome. Since its discovery over two decades ago, γTuRC has evaded in vitro reconstitution and thus detailed structure-function studies. Here, we show that a complex of RuvB-like protein 1 (RUVBL1) and RUVBL2 "RUVBL" controls assembly and composition of γTuRC in human cells. Likewise, RUVBL assembles γTuRC from a minimal set of core subunits in a heterologous coexpression system. RUVBL interacts with γTuRC subcomplexes but is not part of fully assembled γTuRC. Purified, reconstituted γTuRC has nucleation activity and resembles native γTuRC as revealed by its cryo-electron microscopy (cryo-EM) structure at ~4.0-Å resolution. We further use cryo-EM to identify features that determine the intricate, higher-order γTuRC architecture. Our work finds RUVBL as an assembly factor that regulates γTuRC in cells and allows production of recombinant γTuRC for future in-depth mechanistic studies.
History
DepositionOct 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1May 1, 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-11888
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: Tubulin gamma-1 chain
2: Tubulin gamma-1 chain
3: Gamma-tubulin complex component 3
4: Gamma-tubulin complex component 6
5: Mitotic-spindle organizing protein 1
6: Mitotic-spindle organizing protein 1
7: Actin, cytoplasmic 1
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: Gamma-tubulin complex component 3
O: Tubulin gamma-1 chain
P: Tubulin gamma-1 chain
Q: Tubulin gamma-1 chain
R: Tubulin gamma-1 chain
S: Tubulin gamma-1 chain
T: Tubulin gamma-1 chain
U: Tubulin gamma-1 chain
V: Tubulin gamma-1 chain
W: Tubulin gamma-1 chain
X: Tubulin gamma-1 chain
Y: Tubulin gamma-1 chain
Z: Tubulin gamma-1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,583,16847
Polymers2,576,96333
Non-polymers6,20514
Water00
1


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

-
Components

-
Protein , 3 types, 17 molecules 12OPQRSTUVWXYZ567

#1: Protein
Tubulin gamma-1 chain / Gamma-1-tubulin / Gamma-tubulin complex component 1 / GCP-1


Mass: 50741.297 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TUBG1, TUBG / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P23258
#4: Protein Mitotic-spindle organizing protein 1 / Mitotic-spindle organizing protein associated with a ring of gamma-tubulin 1


Mass: 8485.724 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MZT1, C13orf37, MOZART1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q08AG7
#5: Protein Actin, cytoplasmic 1 / Beta-actin


Mass: 41723.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTB / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P60709

-
Gamma-tubulin complex component ... , 5 types, 16 molecules 3BDFHN4LACEGMIKJ

#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.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TUBGCP3, GCP3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96CW5
#3: Protein Gamma-tubulin complex component 6 / GCP-6


Mass: 200733.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TUBGCP6, GCP6, KIAA1669 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96RT7
#6: Protein
Gamma-tubulin complex component 2 / hGCP2 / Gamma-ring complex protein 103 kDa / hGrip103 / Spindle pole body protein Spc97 homolog / hSpc97


Mass: 102666.953 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TUBGCP2, GCP2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BSJ2
#7: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TUBGCP4, 76P, GCP4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UGJ1
#8: Protein Gamma-tubulin complex component 5 / GCP-5


Mass: 118467.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TUBGCP5, GCP5, KIAA1899 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96RT8

-
Non-polymers , 1 types, 14 molecules

#9: Chemical
ChemComp-GDP / GUANOSINE-5'-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: Recombinant human gamma-tubulin ring complex / Type: COMPLEX / Entity ID: #1-#8 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Plasmid: pBIG2
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 58 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 105181 / 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