+Open data
-Basic information
Entry | Database: PDB / ID: 7nvo | |||||||||
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Title | Human TRiC complex in open state with nanobody bound | |||||||||
Components |
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Keywords | CHAPERONE / TRiC / CCT / ATP hydrolysis / type II chaperonin / protein folding | |||||||||
Function / homology | Function and homology information zona pellucida receptor complex / scaRNA localization to Cajal body / 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 / Folding of actin by CCT/TriC / binding of sperm to zona pellucida / Formation of tubulin folding intermediates by CCT/TriC ...zona pellucida receptor complex / scaRNA localization to Cajal body / 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 / Folding of actin by CCT/TriC / binding of sperm to zona pellucida / Formation of tubulin folding intermediates by CCT/TriC / positive regulation of telomerase RNA localization to Cajal body / Prefoldin mediated transfer of substrate to CCT/TriC / chaperonin-containing T-complex / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / WD40-repeat domain binding / pericentriolar material / beta-tubulin binding / Association of TriC/CCT with target proteins during biosynthesis / chaperone-mediated protein complex assembly / RHOBTB2 GTPase cycle / heterochromatin / chaperone-mediated protein folding / protein folding chaperone / : / positive regulation of telomere maintenance via telomerase / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / acrosomal vesicle / cell projection / mRNA 3'-UTR binding / ATP-dependent protein folding chaperone / response to virus / mRNA 5'-UTR binding / cilium / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / G-protein beta-subunit binding / azurophil granule lumen / unfolded protein binding / melanosome / protein folding / cell body / secretory granule lumen / microtubule / ficolin-1-rich granule lumen / cytoskeleton / protein stabilization / cadherin binding / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / Golgi apparatus / ATP hydrolysis activity / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Lama glama (llama) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Kelly, J.J. / Chi, G. / Bulawa, C. / Paavilainen, V.O. / Bountra, C. / Huiskonen, J.T. / Yue, W. | |||||||||
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 | 7nvo.cif.gz | 826.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nvo.ent.gz | 636.5 KB | Display | PDB format |
PDBx/mmJSON format | 7nvo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nvo_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 7nvo_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 7nvo_validation.xml.gz | 124 KB | Display | |
Data in CIF | 7nvo_validation.cif.gz | 187.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/7nvo ftp://data.pdbj.org/pub/pdb/validation_reports/nv/7nvo | HTTPS FTP |
-Related structure data
Related structure data | 12608MC 7nvlC 7nvmC 7nvnC 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 EeHhQqZzGgAaDdBb
#1: 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 #2: Protein | Mass: 59443.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q99832 #3: Protein | Mass: 59691.422 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P50990 #4: Protein | Mass: 58106.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P40227 #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: 60418.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P17987 #7: Protein | Mass: 57996.113 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P50991 #8: Protein | Mass: 57567.141 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P78371 |
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-Antibody , 1 types, 2 molecules Nn
#9: 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, 54 molecules
#10: Chemical | ChemComp-MG / #11: Chemical | ChemComp-ADP / #12: Chemical | ChemComp-AF3 / #13: 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
Component |
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Molecular weight |
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Source (natural) |
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Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||||||
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
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 144903 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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