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Yorodumi- PDB-7nvm: Human TRiC complex in closed state with nanobody Nb18, actin and ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nvm | |||||||||
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Title | Human TRiC complex in closed state with nanobody Nb18, actin and PhLP2A bound | |||||||||
Components |
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Keywords | CHAPERONE / TRiC / CCT / ATP hydrolysis / type II chaperonin / protein folding / actin / Structural Genomics / Structural Genomics Consortium / SGC | |||||||||
Function / homology | Function and homology information basal body patch / negative regulation of chaperone-mediated protein folding / perinucleolar compartment / tight junction assembly / regulation of transepithelial transport / zona pellucida receptor complex / structural constituent of postsynaptic actin cytoskeleton / protein localization to bicellular tight junction / scaRNA localization to Cajal body / morphogenesis of a polarized epithelium ...basal body patch / negative regulation of chaperone-mediated protein folding / perinucleolar compartment / tight junction assembly / regulation of transepithelial transport / zona pellucida receptor complex / structural constituent of postsynaptic actin cytoskeleton / protein localization to bicellular tight junction / scaRNA localization to Cajal body / morphogenesis of a polarized epithelium / profilin binding / positive regulation of protein localization to Cajal body / tubulin complex assembly / Formation of annular gap junctions / chaperone mediated protein folding independent of cofactor / positive regulation of establishment of protein localization to telomere / Gap junction degradation / BBSome-mediated cargo-targeting to cilium / dense body / Cell-extracellular matrix interactions / chaperonin-containing T-complex / Folding of actin by CCT/TriC / positive regulation of telomerase RNA localization to Cajal body / Formation of tubulin folding intermediates by CCT/TriC / vascular endothelial growth factor receptor 2 binding / binding of sperm to zona pellucida / Prefoldin mediated transfer of substrate to CCT/TriC / regulation of stress fiber assembly / Adherens junctions interactions / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / sarcomere organization / NuA4 histone acetyltransferase complex / WD40-repeat domain binding / regulation of synaptic vesicle endocytosis / apical junction complex / regulation of focal adhesion assembly / maintenance of blood-brain barrier / positive regulation of wound healing / myofibril / beta-tubulin binding / pericentriolar material / Recycling pathway of L1 / filamentous actin / Association of TriC/CCT with target proteins during biosynthesis / calyx of Held / EPH-ephrin mediated repulsion of cells / chaperone-mediated protein complex assembly / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / heterochromatin / RHOBTB2 GTPase cycle / phagocytic vesicle / chaperone-mediated protein folding / protein folding chaperone / regulation of peptidyl-tyrosine phosphorylation / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of telomerase activity / positive regulation of telomere maintenance via telomerase / EPHB-mediated forward signaling / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / positive regulation of endothelial cell proliferation / axonogenesis / acrosomal vesicle / mRNA 3'-UTR binding / cell projection / actin filament / cell motility / RHO GTPases Activate Formins / Translocation of SLC2A4 (GLUT4) to the plasma membrane / FCGR3A-mediated phagocytosis / ATP-dependent protein folding chaperone / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / response to virus / Signaling by high-kinase activity BRAF mutants / Schaffer collateral - CA1 synapse / MAP2K and MAPK activation / mRNA 5'-UTR binding / cilium / structural constituent of cytoskeleton / Regulation of actin dynamics for phagocytic cup formation / platelet aggregation / VEGFA-VEGFR2 Pathway / cellular response to type II interferon / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / G-protein beta-subunit binding / positive regulation of angiogenesis / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / azurophil granule lumen / melanosome / cell-cell junction / unfolded protein binding / Signaling by BRAF and RAF1 fusions / protein folding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Lama glama (llama) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Kelly, J.J. / Chi, G. / Bulawa, C. / Paavilainen, V.O. / Bountra, C. / Huiskonen, J.T. / Yue, W. / Structural Genomics Consortium (SGC) | |||||||||
Funding support | United Kingdom, Finland, 2items
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Citation | Journal: Nat Struct Mol Biol / Year: 2022 Title: Snapshots of actin and tubulin folding inside the TRiC chaperonin. Authors: John J Kelly / Dale Tranter / Els Pardon / Gamma Chi / Holger Kramer / Lotta Happonen / Kelly M Knee / Jay M Janz / Jan Steyaert / Christine Bulawa / Ville O Paavilainen / Juha T Huiskonen / Wyatt W Yue / Abstract: The integrity of a cell's proteome depends on correct folding of polypeptides by chaperonins. The chaperonin TCP-1 ring complex (TRiC) acts as obligate folder for >10% of cytosolic proteins, ...The integrity of a cell's proteome depends on correct folding of polypeptides by chaperonins. The chaperonin TCP-1 ring complex (TRiC) acts as obligate folder for >10% of cytosolic proteins, including he cytoskeletal proteins actin and tubulin. Although its architecture and how it recognizes folding substrates are emerging from structural studies, the subsequent fate of substrates inside the TRiC chamber is not defined. We trapped endogenous human TRiC with substrates (actin, tubulin) and cochaperone (PhLP2A) at different folding stages, for structure determination by cryo-EM. The already-folded regions of client proteins are anchored at the chamber wall, positioning unstructured regions toward the central space to achieve their native fold. Substrates engage with different sections of the chamber during the folding cycle, coupled to TRiC open-and-close transitions. Further, the cochaperone PhLP2A modulates folding, acting as a molecular strut between substrate and TRiC chamber. Our structural snapshots piece together an emerging model of client protein folding within TRiC. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7nvm.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7nvm.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 7nvm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/7nvm ftp://data.pdbj.org/pub/pdb/validation_reports/nv/7nvm | HTTPS FTP |
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-Related structure data
Related structure data | 12606MC 7nvlC 7nvnC 7nvoC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-T-complex protein 1 subunit ... , 8 types, 16 molecules AaBbDdEeGgHhQqZz
#1: Protein | Mass: 60418.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P17987 #2: Protein | Mass: 57567.141 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P78371 #3: Protein | Mass: 57996.113 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P50991 #4: Protein | Mass: 59749.957 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCT5, CCTE, KIAA0098 / Production host: Homo sapiens (human) / References: UniProt: P48643 #5: Protein | Mass: 60613.855 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCT3, CCTG, TRIC5 / Production host: Homo sapiens (human) / References: UniProt: P49368 #6: Protein | Mass: 59443.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q99832 #8: Protein | Mass: 59691.422 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P50990 #9: Protein | Mass: 58106.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P40227 |
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-Protein , 2 types, 2 molecules KP
#10: Protein | Mass: 41838.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63261 |
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#11: Protein | Mass: 27650.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H2J4 |
-Antibody , 1 types, 2 molecules Nn
#7: Antibody | Mass: 14412.816 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) |
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-Non-polymers , 4 types, 67 molecules
#12: Chemical | ChemComp-ADP / #13: Chemical | ChemComp-MG / #14: Chemical | ChemComp-AF3 / #15: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | 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
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
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 |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 43 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 63082 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.38 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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