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Open data
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Basic information
Entry | Database: PDB / ID: 7x0s | ||||||
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Title | Human TRiC-tubulin-S3 | ||||||
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![]() | STRUCTURAL PROTEIN | ||||||
Function / homology | ![]() odontoblast differentiation / 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 / cytoskeleton-dependent intracellular transport / Folding of actin by CCT/TriC ...odontoblast differentiation / 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 / cytoskeleton-dependent intracellular transport / Folding of actin by CCT/TriC / binding of sperm to zona pellucida / positive regulation of telomerase RNA localization to Cajal body / Formation of tubulin folding intermediates by CCT/TriC / natural killer cell mediated cytotoxicity / Prefoldin mediated transfer of substrate to CCT/TriC / chaperonin-containing T-complex / GTPase activating protein binding / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / WD40-repeat domain binding / intercellular bridge / regulation of synapse organization / pericentriolar material / nuclear envelope lumen / beta-tubulin binding / MHC class I protein binding / Association of TriC/CCT with target proteins during biosynthesis / microtubule-based process / chaperone-mediated protein complex assembly / spindle assembly / RHOBTB2 GTPase cycle / heterochromatin / chaperone-mediated protein folding / protein folding chaperone / 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 / positive regulation of telomere maintenance via telomerase / Anchoring of the basal body to the plasma membrane / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / AURKA Activation by TPX2 / acrosomal vesicle / mRNA 3'-UTR binding / cell projection / ATP-dependent protein folding chaperone / response to virus / structural constituent of cytoskeleton / mitotic spindle / mRNA 5'-UTR binding / cilium / cytoplasmic ribonucleoprotein granule / microtubule cytoskeleton organization / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / G-protein beta-subunit binding / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / azurophil granule lumen / unfolded protein binding / melanosome / protein folding / mitotic cell cycle / cell body / secretory granule lumen / microtubule / ficolin-1-rich granule lumen / Potential therapeutics for SARS / cytoskeleton / protein stabilization / cadherin binding / membrane raft / protein domain specific binding / cell division / GTPase activity / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / protein-containing complex binding / GTP binding / structural molecule activity / Golgi apparatus / ATP hydrolysis activity / protein-containing complex / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
![]() | Cong, Y. / Liu, C.X. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Pathway and mechanism of tubulin folding mediated by TRiC/CCT along its ATPase cycle revealed using cryo-EM. Authors: Caixuan Liu / Mingliang Jin / Shutian Wang / Wenyu Han / Qiaoyu Zhao / Yifan Wang / Cong Xu / Lei Diao / Yue Yin / Chao Peng / Lan Bao / Yanxing Wang / Yao Cong / ![]() Abstract: The eukaryotic chaperonin TRiC/CCT assists the folding of about 10% of cytosolic proteins through an ATP-driven conformational cycle, and the essential cytoskeleton protein tubulin is the obligate ...The eukaryotic chaperonin TRiC/CCT assists the folding of about 10% of cytosolic proteins through an ATP-driven conformational cycle, and the essential cytoskeleton protein tubulin is the obligate substrate of TRiC. Here, we present an ensemble of cryo-EM structures of endogenous human TRiC throughout its ATPase cycle, with three of them revealing endogenously engaged tubulin in different folding stages. The open-state TRiC-tubulin-S1 and -S2 maps show extra density corresponding to tubulin in the cis-ring chamber of TRiC. Our structural and XL-MS analyses suggest a gradual upward translocation and stabilization of tubulin within the TRiC chamber accompanying TRiC ring closure. In the closed TRiC-tubulin-S3 map, we capture a near-natively folded tubulin-with the tubulin engaging through its N and C domains mainly with the A and I domains of the CCT3/6/8 subunits through electrostatic and hydrophilic interactions. Moreover, we also show the potential role of TRiC C-terminal tails in substrate stabilization and folding. Our study delineates the pathway and molecular mechanism of TRiC-mediated folding of tubulin along the ATPase cycle of TRiC, and may also inform the design of therapeutic agents targeting TRiC-tubulin interactions. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 1.4 MB | Display | ![]() |
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PDB format | ![]() | 1.2 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 199 KB | Display | |
Data in CIF | ![]() | 307.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 32923MC ![]() 7wz3C ![]() 7x0aC ![]() 7x0vC ![]() 7x3jC ![]() 7x3uC ![]() 7x6qC ![]() 7x7yC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 KzJPHOGNEeIMBLAa
#1: Protein | Mass: 58106.086 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 59691.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Protein | Mass: 59417.457 Da / Num. of mol.: 2 / Mutation: L290S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #4: Protein | Mass: 60613.855 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #5: Protein | Mass: 59547.684 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #6: Protein | Mass: 57996.113 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #7: Protein | Mass: 57567.141 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #8: Protein | Mass: 60418.477 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Protein , 1 types, 1 molecules R
#9: Protein | Mass: 49717.629 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Non-polymers , 4 types, 64 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/AF3.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/AF3.gif)
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#10: Chemical | ChemComp-ADP / #11: Chemical | ChemComp-MG / #12: Chemical | ChemComp-AF3 / #13: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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
Component | Name: Human TRiC-tubulin-S3 / Type: COMPLEX / Entity ID: #1-#9 / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Buffer component | Conc.: 50 mM / Name: sodium Chloride / Formula: NaCl |
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: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 38 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103406 / Symmetry type: POINT |