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- PDB-8vrk: Rigid body fitted model for refined density map of gamma tubulin ... -
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Basic information
Entry | Database: PDB / ID: 8vrk | ||||||
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Title | Rigid body fitted model for refined density map of gamma tubulin ring complex capped microtubule | ||||||
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![]() | CELL CYCLE / Microtubule nucleation complex bound to a microtubule | ||||||
Function / homology | ![]() netrin receptor binding / microtubule nucleation by interphase microtubule organizing center / gamma-tubulin complex localization / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / equatorial microtubule organizing center / Post-chaperonin tubulin folding pathway / regulation of transepithelial transport / microtubule minus-end binding / dorsal root ganglion development ...netrin receptor binding / microtubule nucleation by interphase microtubule organizing center / gamma-tubulin complex localization / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / equatorial microtubule organizing center / Post-chaperonin tubulin folding pathway / regulation of transepithelial transport / microtubule minus-end binding / dorsal root ganglion development / morphogenesis of a polarized epithelium / mitotic spindle microtubule / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / gamma-tubulin ring complex / Cilium Assembly / bBAF complex / interphase microtubule organizing center / Carboxyterminal post-translational modifications of tubulin / polar microtubule / postsynaptic actin cytoskeleton organization / npBAF complex / gamma-tubulin complex / nBAF complex / protein localization to adherens junction / brahma complex / postsynaptic actin cytoskeleton / Tat protein binding / structural constituent of postsynaptic actin cytoskeleton / meiotic spindle organization / Sealing of the nuclear envelope (NE) by ESCRT-III / GBAF complex / Intraflagellar transport / dense body / Formation of annular gap junctions / regulation of G0 to G1 transition / cytoskeleton-dependent intracellular transport / Gap junction degradation / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / Regulation of MITF-M-dependent genes involved in pigmentation / Formation of tubulin folding intermediates by CCT/TriC / microtubule nucleation / apical protein localization / Gap junction assembly / regulation of double-strand break repair / COPI-independent Golgi-to-ER retrograde traffic / adherens junction assembly / regulation of nucleotide-excision repair / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / gamma-tubulin binding / RHOF GTPase cycle / non-motile cilium / Adherens junctions interactions / Assembly and cell surface presentation of NMDA receptors / tight junction / Kinesins / Sensory processing of sound by outer hair cells of the cochlea / regulation of norepinephrine uptake / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of double-strand break repair / regulation of synaptic vesicle endocytosis / microtubule organizing center / positive regulation of T cell differentiation / apical junction complex / COPI-dependent Golgi-to-ER retrograde traffic / establishment or maintenance of cell polarity / regulation of cyclin-dependent protein serine/threonine kinase activity / intercellular bridge / cortical cytoskeleton / maintenance of blood-brain barrier / positive regulation of stem cell population maintenance / pericentriolar material / NuA4 histone acetyltransferase complex / nitric-oxide synthase binding / cell leading edge / cytoplasmic microtubule / regulation of G1/S transition of mitotic cell cycle / Recycling pathway of L1 / mitotic sister chromatid segregation / kinesin binding / brush border / calyx of Held / microtubule-based process / negative regulation of cell differentiation / RHOH GTPase cycle / mitotic spindle assembly / positive regulation of double-strand break repair via homologous recombination / single fertilization / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / spindle assembly / regulation of protein localization to plasma membrane / positive regulation of myoblast differentiation / cellular response to interleukin-4 / Hedgehog 'off' state Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.5 Å | ||||||
![]() | Aher, A. / Urnavicius, L. / Kapoor, T.M. | ||||||
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 3.5 MB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 43483MC ![]() 8vrjC ![]() 8vt7C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 8 types, 53 molecules 1OPQRSTUVWXYZ2opqrstuvwxyz36L7...
#1: Protein | Mass: 51019.297 Da / Num. of mol.: 13 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P68363, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement #2: Protein | Mass: 51276.367 Da / Num. of mol.: 13 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Protein | Mass: 199732.516 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #5: Protein | Mass: 8485.724 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #6: Protein | | Mass: 41782.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #7: Protein | Mass: 105581.500 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #8: Protein | Mass: 76108.898 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #10: Protein | Mass: 52022.617 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Gamma-tubulin complex component ... , 2 types, 7 molecules 5BDFHNJ
#4: Protein | Mass: 103710.102 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #9: Protein | | Mass: 118367.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Gamma tubulin ring complex bound to microtubule minus end Type: COMPLEX / Entity ID: #10, #1-#9 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 6.8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 8.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9856 / Symmetry type: POINT |