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- PDB-7nvn: Human TRiC complex in closed state with nanobody and tubulin bound -
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Basic information
Entry | Database: PDB / ID: 7nvn | ||||||
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Title | Human TRiC complex in closed state with nanobody and tubulin bound | ||||||
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![]() | CHAPERONE / TRiC / CCT / ATP hydrolysis / type II chaperonin / protein folding / tubulin | ||||||
Function / homology | ![]() Post-chaperonin tubulin folding pathway / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / 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 ...Post-chaperonin tubulin folding pathway / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / 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 / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / 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 / Gap junction assembly / COPI-independent Golgi-to-ER retrograde traffic / Prefoldin mediated transfer of substrate to CCT/TriC / chaperonin-containing T-complex / Assembly and cell surface presentation of NMDA receptors / Kinesins / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / WD40-repeat domain binding / COPI-dependent Golgi-to-ER retrograde traffic / pericentriolar material / beta-tubulin binding / Recycling pathway of L1 / Association of TriC/CCT with target proteins during biosynthesis / 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 / chaperone-mediated protein folding / Mitotic Prometaphase / protein folding chaperone / EML4 and NUDC in mitotic spindle formation / positive regulation of telomerase activity / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / positive regulation of telomere maintenance via telomerase / 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 / mRNA 3'-UTR binding / cell projection / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / ATP-dependent protein folding chaperone / neuron migration / response to virus / structural constituent of cytoskeleton / cilium / mRNA 5'-UTR binding / Aggrephagy / microtubule cytoskeleton organization / HCMV Early Events / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / G-protein beta-subunit binding / azurophil granule lumen / extracellular vesicle / unfolded protein binding / melanosome / protein folding / mitotic cell cycle / cell body / secretory granule lumen / microtubule / ficolin-1-rich granule lumen / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
![]() | Kelly, J.J. / Chi, G. / Bulawa, C. / Paavilainen, V.O. / Bountra, C. / Huiskonen, J.T. / Yue, W. | ||||||
![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 1.5 MB | Display | ![]() |
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PDB format | ![]() | 1.2 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 214.3 KB | Display | |
Data in CIF | ![]() | 329.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 12607MC ![]() 7nvlC ![]() 7nvmC ![]() 7nvoC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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) ![]() #2: Protein | Mass: 57567.141 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | Mass: 57996.113 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Protein | Mass: 59749.957 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #5: Protein | Mass: 60613.855 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #6: Protein | Mass: 59443.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #8: Protein | Mass: 59691.422 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #9: Protein | Mass: 58106.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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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) ![]() |
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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.) ![]() ![]() ![]() ![]() |
-Non-polymers , 4 types, 67 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/AF3.gif)
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#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 |
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Sample preparation
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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 |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 43 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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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 | ||||||||||||||||||||||||
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