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Basic information

Entry
Database: PDB / ID: 8vrk
TitleRigid body fitted model for refined density map of gamma tubulin ring complex capped microtubule
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 alpha-1B chain
  • Tubulin beta-3 chain
  • Tubulin gamma-1 chain
KeywordsCELL CYCLE / Microtubule nucleation complex bound to a microtubule
Function / homology
Function and homology information


netrin receptor binding / microtubule nucleation by interphase microtubule organizing center / gamma-tubulin complex localization / microtubule nucleator activity / dorsal root ganglion development / Post-chaperonin tubulin folding pathway / positive regulation of norepinephrine uptake / Cilium Assembly / cytoskeleton-dependent intracellular transport / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane ...netrin receptor binding / microtubule nucleation by interphase microtubule organizing center / gamma-tubulin complex localization / microtubule nucleator activity / dorsal root ganglion development / Post-chaperonin tubulin folding pathway / positive regulation of norepinephrine uptake / Cilium Assembly / cytoskeleton-dependent intracellular transport / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Carboxyterminal post-translational modifications of tubulin / polar microtubule / interphase microtubule organizing center / gamma-tubulin complex / gamma-tubulin ring complex / cellular response to cytochalasin B / bBAF complex / mitotic spindle microtubule / Intraflagellar transport / Sealing of the nuclear envelope (NE) by ESCRT-III / npBAF complex / nBAF complex / brahma complex / meiotic spindle organization / Formation of tubulin folding intermediates by CCT/TriC / regulation of transepithelial transport / Formation of annular gap junctions / morphogenesis of a polarized epithelium / Formation of the dystrophin-glycoprotein complex (DGC) / structural constituent of postsynaptic actin cytoskeleton / Gap junction degradation / GBAF complex / Folding of actin by CCT/TriC / regulation of G0 to G1 transition / protein localization to adherens junction / Cell-extracellular matrix interactions / Gap junction assembly / microtubule nucleation / dense body / postsynaptic actin cytoskeleton / Tat protein binding / gamma-tubulin binding / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / regulation of double-strand break repair / regulation of nucleotide-excision repair / Kinesins / non-motile cilium / Adherens junctions interactions / RHOF GTPase cycle / adherens junction assembly / COPI-independent Golgi-to-ER retrograde traffic / Assembly and cell surface presentation of NMDA receptors / apical protein localization / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / tight junction / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / Sensory processing of sound by inner hair cells of the cochlea / COPI-dependent Golgi-to-ER retrograde traffic / 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 / nitric-oxide synthase binding / cortical cytoskeleton / NuA4 histone acetyltransferase complex / establishment or maintenance of cell polarity / pericentriolar material / positive regulation of stem cell population maintenance / cell leading edge / Regulation of MITF-M-dependent genes involved in pigmentation / Recycling pathway of L1 / microtubule organizing center / brush border / mitotic sister chromatid segregation / regulation of G1/S transition of mitotic cell cycle / RHOH GTPase cycle / EPH-ephrin mediated repulsion of cells / kinesin binding / negative regulation of cell differentiation / mitotic spindle assembly / RHO GTPases Activate WASPs and WAVEs / regulation of synaptic vesicle endocytosis / positive regulation of myoblast differentiation / single fertilization / RHO GTPases activate IQGAPs / microtubule-based process / regulation of protein localization to plasma membrane / Hedgehog 'off' state / positive regulation of double-strand break repair via homologous recombination / intercellular bridge / COPI-mediated anterograde transport / Activation of AMPK downstream of NMDARs / spindle assembly / cytoplasmic microtubule / cytoplasmic microtubule organization
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 / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Actins signature 1. / Beta tubulin / 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
Gamma-tubulin complex component 6 / Tubulin gamma-1 chain / Actin, cytoplasmic 1 / Tubulin alpha-1B chain / Mitotic-spindle organizing protein 1 / Tubulin beta-3 chain / 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: 8.5 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 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 31, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Tubulin alpha-1B chain
2: Tubulin beta-3 chain
3: TUBGCP6 protein
5: Gamma-tubulin complex component 3
6: TUBGCP6 protein
7: Mitotic-spindle organizing protein 1
8: Mitotic-spindle organizing protein 1
9: Actin, cytoplasmic 1
A: Isoform 3 of Gamma-tubulin complex component 2
B: Gamma-tubulin complex component 3
C: Isoform 3 of Gamma-tubulin complex component 2
D: Gamma-tubulin complex component 3
E: Isoform 3 of Gamma-tubulin complex component 2
F: Gamma-tubulin complex component 3
G: Isoform 3 of Gamma-tubulin complex component 2
H: Gamma-tubulin complex component 3
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
M: Isoform 3 of Gamma-tubulin complex component 2
N: Gamma-tubulin complex component 3
O: Tubulin alpha-1B chain
P: Tubulin alpha-1B chain
Q: Tubulin alpha-1B chain
R: Tubulin alpha-1B chain
S: Tubulin alpha-1B chain
T: Tubulin alpha-1B chain
U: Tubulin alpha-1B chain
V: Tubulin alpha-1B chain
W: Tubulin alpha-1B chain
X: Tubulin alpha-1B chain
Y: Tubulin alpha-1B chain
Z: Tubulin alpha-1B chain
o: Tubulin beta-3 chain
p: Tubulin beta-3 chain
q: Tubulin beta-3 chain
r: Tubulin beta-3 chain
s: Tubulin beta-3 chain
t: Tubulin beta-3 chain
u: Tubulin beta-3 chain
v: Tubulin beta-3 chain
w: Tubulin beta-3 chain
x: Tubulin beta-3 chain
y: Tubulin beta-3 chain
z: Tubulin beta-3 chain
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
n: Tubulin gamma-1 chain


Theoretical massNumber of molelcules
Total (without water)4,136,86560
Polymers4,136,86560
Non-polymers00
Water00
1


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

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Components

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Protein , 8 types, 53 molecules 1OPQRSTUVWXYZ2opqrstuvwxyz36L7...

#1: Protein
Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 51019.297 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TUBA1B / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P68363, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: Protein
Tubulin beta-3 chain / Tubulin beta-4 chain / Tubulin beta-III


Mass: 51276.367 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TUBB3, TUBB4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13509
#3: 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
#5: 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
#6: 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
#7: 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
#8: 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
#10: 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

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Gamma-tubulin complex component ... , 2 types, 7 molecules 5BDFHNJ

#4: 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
#9: 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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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 bound to microtubule minus end
Type: COMPLEX / Entity ID: #10, #1-#9 / 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

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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: 8.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9856 / Symmetry type: POINT

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