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Yorodumi- PDB-8vrd: Rigid body fitted model for free recombinant gamma tubulin ring c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vrd | ||||||
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Title | Rigid body fitted model for free recombinant gamma tubulin ring complex. | ||||||
Components |
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Keywords | CYTOSOLIC PROTEIN / Complex | ||||||
Function / homology | Function and homology information 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 / mitotic spindle microtubule / regulation of transepithelial transport / morphogenesis of a polarized epithelium / gamma-tubulin ring complex / bBAF complex ...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 / mitotic spindle microtubule / regulation of transepithelial transport / morphogenesis of a polarized epithelium / gamma-tubulin ring complex / bBAF complex / interphase microtubule organizing center / postsynaptic actin cytoskeleton organization / polar microtubule / npBAF complex / protein localization to adherens junction / nBAF complex / postsynaptic actin cytoskeleton / brahma complex / meiotic spindle organization / gamma-tubulin complex / Tat protein binding / structural constituent of postsynaptic actin cytoskeleton / GBAF complex / regulation of G0 to G1 transition / Formation of annular gap junctions / dense body / Gap junction degradation / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / apical protein localization / microtubule nucleation / regulation of double-strand break repair / regulation of nucleotide-excision repair / adherens junction assembly / RSC-type complex / Prefoldin mediated transfer of substrate to CCT/TriC / gamma-tubulin binding / non-motile cilium / RHOF GTPase cycle / Adherens junctions interactions / tight junction / regulation of mitotic metaphase/anaphase transition / Interaction between L1 and Ankyrins / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / SWI/SNF complex / microtubule organizing center / regulation of norepinephrine uptake / positive regulation of double-strand break repair / positive regulation of T cell differentiation / regulation of synaptic vesicle endocytosis / apical junction complex / establishment or maintenance of cell polarity / regulation of cyclin-dependent protein serine/threonine kinase activity / cortical cytoskeleton / maintenance of blood-brain barrier / NuA4 histone acetyltransferase complex / positive regulation of stem cell population maintenance / pericentriolar material / nitric-oxide synthase binding / cell leading edge / cytoplasmic microtubule / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of G1/S transition of mitotic cell cycle / Recycling pathway of L1 / brush border / mitotic sister chromatid segregation / kinesin binding / negative regulation of cell differentiation / calyx of Held / positive regulation of double-strand break repair via homologous recombination / EPH-ephrin mediated repulsion of cells / mitotic spindle assembly / single fertilization / positive regulation of myoblast differentiation / regulation of protein localization to plasma membrane / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / spindle assembly / 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 / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / substantia nigra development / EPHB-mediated forward signaling / centriole / AURKA Activation by TPX2 / axonogenesis / mitotic spindle organization / ciliary basal body / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / platelet aggregation / negative regulation of protein binding / condensed nuclear chromosome / meiotic cell cycle / cell motility / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7 Å | ||||||
Authors | Aher, A. / Urnavicius, L. / Kapoor, T.M. | ||||||
Funding support | United States, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8vrd.cif.gz | 2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8vrd.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 8vrd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vrd_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8vrd_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8vrd_validation.xml.gz | 245.3 KB | Display | |
Data in CIF | 8vrd_validation.cif.gz | 428.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/8vrd ftp://data.pdbj.org/pub/pdb/validation_reports/vr/8vrd | HTTPS FTP |
-Related structure data
Related structure data | 43481MC 8va2C 8vrjC 8vrkC 8vt7C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Gamma-tubulin complex component ... , 2 types, 7 molecules OBDFHNJ
#1: 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 #8: 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 |
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-Protein , 6 types, 27 molecules PLTQRSACEGMabcdefghijklmnIK
#2: 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 | 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 | | 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 | 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 | 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 | 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 modification | N |
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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 |
-Sample preparation
Component | Name: Gamma tubulin ring complex / Type: COMPLEX / Entity ID: #5, #1, #7-#8, #2-#4, #6 / Source: RECOMBINANT |
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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 / Humidity: 100 % |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
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) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98558 / Symmetry type: POINT |
Atomic model building | Protocol: RIGID BODY FIT |