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- PDB-8vrd: Rigid body fitted model for free recombinant gamma tubulin ring c... -

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Basic information

Entry
Database: PDB / ID: 8vrd
TitleRigid body fitted model for free recombinant gamma tubulin ring complex.
Components
  • (Gamma-tubulin complex component ...) x 2
  • Actin, cytoplasmic 1
  • Isoform 2 of Gamma-tubulin complex component 4
  • Isoform 3 of Gamma-tubulin complex component 2
  • Mitotic-spindle organizing protein 1
  • TUBGCP6 protein
  • Tubulin gamma-1 chain
KeywordsCYTOSOLIC PROTEIN / Complex
Function / homology
Function and homology information


microtubule nucleation by interphase microtubule organizing center / equatorial microtubule organizing center / gamma-tubulin complex localization / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / bBAF complex / gamma-tubulin ring complex / polar microtubule / npBAF complex / interphase microtubule organizing center ...microtubule nucleation by interphase microtubule organizing center / equatorial microtubule organizing center / gamma-tubulin complex localization / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / bBAF complex / gamma-tubulin ring complex / polar microtubule / npBAF complex / interphase microtubule organizing center / regulation of transepithelial transport / nBAF complex / brahma complex / gamma-tubulin complex / meiotic spindle organization / mitotic spindle microtubule / morphogenesis of a polarized epithelium / protein localization to adherens junction / postsynaptic actin cytoskeleton / structural constituent of postsynaptic actin cytoskeleton / GBAF complex / Formation of annular gap junctions / regulation of G0 to G1 transition / Gap junction degradation / Tat protein binding / Folding of actin by CCT/TriC / Cell-extracellular matrix interactions / dense body / regulation of double-strand break repair / microtubule nucleation / regulation of nucleotide-excision repair / Prefoldin mediated transfer of substrate to CCT/TriC / apical protein localization / RSC-type complex / adherens junction assembly / gamma-tubulin binding / Adherens junctions interactions / RHOF GTPase cycle / non-motile cilium / tight junction / Sensory processing of sound by outer hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / positive regulation of double-strand break repair / positive regulation of T cell differentiation / regulation of norepinephrine uptake / apical junction complex / nitric-oxide synthase binding / microtubule organizing center / regulation of cyclin-dependent protein serine/threonine kinase activity / maintenance of blood-brain barrier / establishment or maintenance of cell polarity / NuA4 histone acetyltransferase complex / pericentriolar material / cortical cytoskeleton / positive regulation of stem cell population maintenance / cytoplasmic microtubule / cell leading edge / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of synaptic vesicle endocytosis / regulation of G1/S transition of mitotic cell cycle / Recycling pathway of L1 / mitotic sister chromatid segregation / brush border / kinesin binding / negative regulation of cell differentiation / EPH-ephrin mediated repulsion of cells / mitotic spindle assembly / single fertilization / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / positive regulation of myoblast differentiation / spindle assembly / positive regulation of double-strand break repair via homologous recombination / regulation of protein localization to plasma membrane / 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 / substantia nigra development / calyx of Held / EPHB-mediated forward signaling / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / centriole / axonogenesis / mitotic spindle organization / negative regulation of protein binding / AURKA Activation by TPX2 / ciliary basal body / condensed nuclear chromosome / meiotic cell cycle / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / actin filament / adherens junction / positive regulation of cell differentiation / RHO GTPases Activate Formins
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 / Gamma tubulin complex component protein, N-terminal ...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. / Actin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / 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
TUBGCP6 protein / Tubulin gamma-1 chain / Actin, cytoplasmic 1 / Mitotic-spindle organizing protein 1 / Gamma-tubulin complex component 3 / 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: 7 Å
AuthorsAher, A. / Urnavicius, L. / Kapoor, T.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)GM130234 United States
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Structure of the γ-tubulin ring complex-capped microtubule.
Authors: Amol Aher / Linas Urnavicius / Allen Xue / Kasahun Neselu / Tarun M Kapoor /
Abstract: Microtubules are composed of α-tubulin and β-tubulin dimers positioned head-to-tail to form protofilaments that associate laterally in varying numbers. It is not known how cellular microtubules ...Microtubules are composed of α-tubulin and β-tubulin dimers positioned head-to-tail to form protofilaments that associate laterally in varying numbers. It is not known how cellular microtubules assemble with the canonical 13-protofilament architecture, resulting in micrometer-scale α/β-tubulin tracks for intracellular transport that align with, rather than spiral along, the long axis of the filament. We report that the human ~2.3 MDa γ-tubulin ring complex (γ-TuRC), an essential regulator of microtubule formation that contains 14 γ-tubulins, selectively nucleates 13-protofilament microtubules. Cryogenic electron microscopy reconstructions of γ-TuRC-capped microtubule minus ends reveal the extensive intra-domain and inter-domain motions of γ-TuRC subunits that accommodate luminal bridge components and establish lateral and longitudinal interactions between γ-tubulins and α-tubulins. Our structures suggest that γ-TuRC, an inefficient nucleation template owing to its splayed conformation, can transform into a compacted cap at the microtubule minus end and set the lattice architecture of cellular microtubules.
History
DepositionJan 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
O: Gamma-tubulin complex component 3
P: TUBGCP6 protein
Q: Mitotic-spindle organizing protein 1
R: Mitotic-spindle organizing protein 1
S: Actin, cytoplasmic 1
A: Isoform 3 of Gamma-tubulin complex component 2
a: Tubulin gamma-1 chain
B: Gamma-tubulin complex component 3
b: Tubulin gamma-1 chain
C: Isoform 3 of Gamma-tubulin complex component 2
c: Tubulin gamma-1 chain
D: Gamma-tubulin complex component 3
d: Tubulin gamma-1 chain
E: Isoform 3 of Gamma-tubulin complex component 2
e: Tubulin gamma-1 chain
F: Gamma-tubulin complex component 3
f: Tubulin gamma-1 chain
G: Isoform 3 of Gamma-tubulin complex component 2
g: Tubulin gamma-1 chain
H: Gamma-tubulin complex component 3
h: Tubulin gamma-1 chain
i: Tubulin gamma-1 chain
I: Isoform 2 of Gamma-tubulin complex component 4
J: Gamma-tubulin complex component 5
K: Isoform 2 of Gamma-tubulin complex component 4
L: TUBGCP6 protein
T: TUBGCP6 protein
j: Tubulin gamma-1 chain
k: Tubulin gamma-1 chain
l: Tubulin gamma-1 chain
M: Isoform 3 of Gamma-tubulin complex component 2
m: Tubulin gamma-1 chain
N: Gamma-tubulin complex component 3
n: Tubulin gamma-1 chain


Theoretical massNumber of molelcules
Total (without water)2,807,02234
Polymers2,807,02234
Non-polymers00
Water00
1


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

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Components

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Gamma-tubulin complex component ... , 2 types, 7 molecules OBDFHNJ

#1: 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: Trichoplusia ni (cabbage looper) / References: UniProt: Q96CW5
#8: Protein Gamma-tubulin complex component 5 / GCP-5


Mass: 118367.406 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: Trichoplusia ni (cabbage looper) / References: UniProt: Q96RT8

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Protein , 6 types, 27 molecules PLTQRSACEGMabcdefghijklmnIK

#2: Protein TUBGCP6 protein


Mass: 199732.516 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TUBGCP6 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: B2RWN4
#3: 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: Trichoplusia ni (cabbage looper) / References: UniProt: Q08AG7
#4: Protein Actin, cytoplasmic 1 / Beta-actin


Mass: 41782.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTB / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P60709
#5: Protein
Isoform 3 of Gamma-tubulin complex component 2 / GCP-2 / hGCP2 / Gamma-ring complex protein 103 kDa / h103p / hGrip103 / Spindle pole body protein ...GCP-2 / hGCP2 / Gamma-ring complex protein 103 kDa / h103p / hGrip103 / Spindle pole body protein Spc97 homolog / hSpc97


Mass: 105581.500 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TUBGCP2, GCP2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BSJ2
#6: Protein
Tubulin gamma-1 chain / Gamma-1-tubulin / Gamma-tubulin complex component 1 / GCP-1


Mass: 52022.617 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TUBG1, TUBG / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P23258
#7: Protein Isoform 2 of Gamma-tubulin complex component 4 / GCP-4 / hGCP4 / Gamma-ring complex protein 76 kDa / h76p / hGrip76


Mass: 76108.898 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: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UGJ1

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Details

Has protein modificationN

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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: Gamma tubulin ring complex / Type: COMPLEX / Entity ID: #5, #1, #7-#8, #2-#4, #6 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 6.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98558 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT

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