[English] 日本語
Yorodumi- PDB-8vrk: Rigid body fitted model for refined density map of gamma tubulin ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vrk | ||||||
---|---|---|---|---|---|---|---|
Title | Rigid body fitted model for refined density map of gamma tubulin ring complex capped microtubule | ||||||
Components |
| ||||||
Keywords | CELL 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 / positive regulation of norepinephrine uptake / equatorial microtubule organizing center / Post-chaperonin tubulin folding pathway / cellular response to cytochalasin B / Carboxyterminal post-translational modifications of tubulin / dorsal root ganglion development / 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 / positive regulation of norepinephrine uptake / equatorial microtubule organizing center / Post-chaperonin tubulin folding pathway / cellular response to cytochalasin B / Carboxyterminal post-translational modifications of tubulin / dorsal root ganglion development / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / bBAF complex / mitotic spindle microtubule / gamma-tubulin ring complex / interphase microtubule organizing center / npBAF complex / postsynaptic actin cytoskeleton organization / regulation of transepithelial transport / brahma complex / polar microtubule / nBAF complex / structural constituent of postsynaptic actin cytoskeleton / gamma-tubulin complex / morphogenesis of a polarized epithelium / Formation of annular gap junctions / cytoskeleton-dependent intracellular transport / meiotic spindle organization / GBAF complex / Gap junction degradation / Intraflagellar transport / Sealing of the nuclear envelope (NE) by ESCRT-III / postsynaptic actin cytoskeleton / protein localization to adherens junction / regulation of G0 to G1 transition / dense body / Cell-extracellular matrix interactions / Tat protein binding / Gap junction assembly / Folding of actin by CCT/TriC / regulation of double-strand break repair / microtubule nucleation / Formation of tubulin folding intermediates by CCT/TriC / regulation of nucleotide-excision repair / COPI-independent Golgi-to-ER retrograde traffic / RSC-type complex / apical protein localization / Prefoldin mediated transfer of substrate to CCT/TriC / adherens junction assembly / non-motile cilium / RHOF GTPase cycle / gamma-tubulin binding / Adherens junctions interactions / Kinesins / Assembly and cell surface presentation of NMDA receptors / tight junction / Sensory processing of sound by outer hair cells of the cochlea / SWI/SNF complex / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / regulation of norepinephrine uptake / positive regulation of double-strand break repair / COPI-dependent Golgi-to-ER retrograde traffic / positive regulation of T cell differentiation / microtubule organizing center / NuA4 histone acetyltransferase complex / regulation of synaptic vesicle endocytosis / apical junction complex / maintenance of blood-brain barrier / establishment or maintenance of cell polarity / intercellular bridge / cortical cytoskeleton / positive regulation of double-strand break repair via homologous recombination / positive regulation of stem cell population maintenance / pericentriolar material / nitric-oxide synthase binding / single fertilization / Recycling pathway of L1 / regulation of cyclin-dependent protein serine/threonine kinase activity / cell leading edge / regulation of G1/S transition of mitotic cell cycle / mitotic sister chromatid segregation / negative regulation of cell differentiation / brush border / RHOH GTPase cycle / kinesin binding / calyx of Held / EPH-ephrin mediated repulsion of cells / mitotic spindle assembly / RHO GTPases Activate WASPs and WAVEs / spindle assembly / RHO GTPases activate IQGAPs / positive regulation of myoblast differentiation / Hedgehog 'off' state / cytoplasmic microtubule / regulation of protein localization to plasma membrane / microtubule-based process / COPI-mediated anterograde transport / Activation of AMPK downstream of NMDARs / cytoplasmic microtubule organization Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.5 Å | ||||||
Authors | Aher, A. / Urnavicius, L. / Kapoor, T.M. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8vrk.cif.gz | 3.5 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8vrk.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8vrk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/8vrk ftp://data.pdbj.org/pub/pdb/validation_reports/vr/8vrk | HTTPS FTP |
---|
-Related structure data
Related structure data | 43483MC 8vrjC 8vt7C M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-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.) 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 | 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 | 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 | 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 | | 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 | 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 | 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 | 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 |
---|
-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.) Homo sapiens (human) / Gene: TUBGCP3, GCP3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96CW5 #9: Protein | | 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 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 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 solution | pH: 6.8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / 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) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
---|---|
3D reconstruction | Resolution: 8.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9856 / Symmetry type: POINT |