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Yorodumi- PDB-7nvn: Human TRiC complex in closed state with nanobody and tubulin bound -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nvn | ||||||
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Title | Human TRiC complex in closed state with nanobody and tubulin bound | ||||||
Components |
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Keywords | CHAPERONE / TRiC / CCT / ATP hydrolysis / type II chaperonin / protein folding / tubulin | ||||||
Function / homology | Function and homology information Post-chaperonin tubulin folding pathway / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / zona pellucida receptor complex / Cilium Assembly / scaRNA localization to Cajal body / Carboxyterminal post-translational modifications of tubulin / chaperone mediated protein folding independent of cofactor / positive regulation of establishment of protein localization to telomere / positive regulation of protein localization to Cajal body / tubulin complex assembly ...Post-chaperonin tubulin folding pathway / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / zona pellucida receptor complex / Cilium Assembly / scaRNA localization to Cajal body / Carboxyterminal post-translational modifications of tubulin / chaperone mediated protein folding independent of cofactor / positive regulation of establishment of protein localization to telomere / positive regulation of protein localization to Cajal body / tubulin complex assembly / BBSome-mediated cargo-targeting to cilium / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / binding of sperm to zona pellucida / Folding of actin by CCT/TriC / Formation of tubulin folding intermediates by CCT/TriC / positive regulation of telomerase RNA localization to Cajal body / Gap junction assembly / COPI-independent Golgi-to-ER retrograde traffic / chaperonin-containing T-complex / Prefoldin mediated transfer of substrate to CCT/TriC / Assembly and cell surface presentation of NMDA receptors / Kinesins / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / COPI-dependent Golgi-to-ER retrograde traffic / WD40-repeat domain binding / intercellular bridge / pericentriolar material / beta-tubulin binding / Association of TriC/CCT with target proteins during biosynthesis / : / Recycling pathway of L1 / chaperone-mediated protein complex assembly / RHO GTPases activate IQGAPs / RHOBTB2 GTPase cycle / Hedgehog 'off' state / heterochromatin / COPI-mediated anterograde transport / Activation of AMPK downstream of NMDARs / Mitotic Prometaphase / chaperone-mediated protein folding / EML4 and NUDC in mitotic spindle formation / protein folding chaperone / Recruitment of NuMA to mitotic centrosomes / positive regulation of telomere maintenance via telomerase / Resolution of Sister Chromatid Cohesion / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / acrosomal vesicle / cell projection / mRNA 3'-UTR binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / ATP-dependent protein folding chaperone / HCMV Early Events / response to virus / PKR-mediated signaling / cilium / structural constituent of cytoskeleton / mitotic spindle / cerebral cortex development / mRNA 5'-UTR binding / microtubule cytoskeleton organization / Aggrephagy / Separation of Sister Chromatids / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / The role of GTSE1 in G2/M progression after G2 checkpoint / G-protein beta-subunit binding / microtubule cytoskeleton / azurophil granule lumen / extracellular vesicle / unfolded protein binding / melanosome / protein folding / mitotic cell cycle / cell body / secretory granule lumen / ficolin-1-rich granule lumen / microtubule / cytoskeleton / protein stabilization / cadherin binding / GTPase activity / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / GTP binding / Golgi apparatus / ATP hydrolysis activity / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Lama glama (llama) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
Authors | Kelly, J.J. / Chi, G. / Bulawa, C. / Paavilainen, V.O. / Bountra, C. / Huiskonen, J.T. / Yue, W. | ||||||
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 | 7nvn.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7nvn.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 7nvn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nvn_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 7nvn_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 7nvn_validation.xml.gz | 214.3 KB | Display | |
Data in CIF | 7nvn_validation.cif.gz | 329.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/7nvn ftp://data.pdbj.org/pub/pdb/validation_reports/nv/7nvn | HTTPS FTP |
-Related structure data
Related structure data | 12607MC 7nvlC 7nvmC 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 natural source / Source: (natural) 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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-Antibody / Protein , 2 types, 3 molecules NnT
#10: Protein | Mass: 49921.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13885 |
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#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) |
-Non-polymers , 4 types, 67 molecules
#11: Chemical | ChemComp-ADP / #12: Chemical | ChemComp-MG / #13: Chemical | ChemComp-AF3 / #14: 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 |
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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 FIELD |
Image recording | Electron dose: 43 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 93758 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.26 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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