+Open data
-Basic information
Entry | Database: PDB / ID: 7ylw | ||||||
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Title | yeast TRiC-plp2-tubulin complex at S3 closed TRiC state | ||||||
Components |
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Keywords | CHAPERONE / TRiC/CCT / tubulin / phosducin-like protein | ||||||
Function / homology | Function and homology information cellular response to pheromone / negative regulation of chaperone-mediated protein folding / Association of TriC/CCT with target proteins during biosynthesis / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / chaperone mediated protein folding independent of cofactor / chaperonin-containing T-complex / negative regulation of signal transduction / Neutrophil degranulation / ATP-dependent protein folding chaperone / G-protein beta/gamma-subunit complex binding ...cellular response to pheromone / negative regulation of chaperone-mediated protein folding / Association of TriC/CCT with target proteins during biosynthesis / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / chaperone mediated protein folding independent of cofactor / chaperonin-containing T-complex / negative regulation of signal transduction / Neutrophil degranulation / ATP-dependent protein folding chaperone / G-protein beta/gamma-subunit complex binding / structural constituent of cytoskeleton / microtubule cytoskeleton organization / unfolded protein binding / protein folding / mitotic cell cycle / actin binding / actin cytoskeleton organization / microtubule / regulation of cell cycle / GTPase activity / GTP binding / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.39 Å | ||||||
Authors | Han, W.Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Sci Adv / Year: 2023 Title: Structural basis of plp2-mediated cytoskeletal protein folding by TRiC/CCT. Authors: Wenyu Han / Mingliang Jin / Caixuan Liu / Qiaoyu Zhao / Shutian Wang / Yifan Wang / Yue Yin / Chao Peng / Yanxing Wang / Yao Cong / Abstract: The cytoskeletal proteins tubulin and actin are the obligate substrates of TCP-1 ring complex/Chaperonin containing TCP-1 (TRiC/CCT), and their folding involves co-chaperone. Through cryo-electron ...The cytoskeletal proteins tubulin and actin are the obligate substrates of TCP-1 ring complex/Chaperonin containing TCP-1 (TRiC/CCT), and their folding involves co-chaperone. Through cryo-electron microscopy analysis, we present a more complete picture of TRiC-assisted tubulin/actin folding along TRiC adenosine triphosphatase cycle, under the coordination of co-chaperone plp2. In the open S1/S2 states, plp2 and tubulin/actin engaged within opposite TRiC chambers. Notably, we captured an unprecedented TRiC-plp2-tubulin complex in the closed S3 state, engaged with a folded full-length -tubulin and loaded with a guanosine triphosphate, and a plp2 occupying opposite rings. Another closed S4 state revealed an actin in the intermediate folding state and a plp2. Accompanying TRiC ring closure, plp2 translocation could coordinate substrate translocation on the CCT6 hemisphere, facilitating substrate stabilization and folding. Our findings reveal the folding mechanism of the major cytoskeletal proteins tubulin/actin under the coordination of the biogenesis machinery TRiC and plp2 and extend our understanding of the links between cytoskeletal proteostasis and related human diseases. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ylw.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7ylw.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 7ylw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yl/7ylw ftp://data.pdbj.org/pub/pdb/validation_reports/yl/7ylw | HTTPS FTP |
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-Related structure data
Related structure data | 33919MC 7yluC 7ylvC 7ylxC 7ylyC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 60557.566 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: TCP1, CCT1, YDR212W, YD8142.13, YD8142B.04 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P12612 #2: Protein | Mass: 57276.254 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: CCT2, BIN3, TCP2, YIL142W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39076 #3: Protein | Mass: 57682.410 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: CCT4 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39078 #4: Protein | Mass: 61995.004 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: CCT5, TCP5, YJR064W, J1752 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40413 #5: Protein | Mass: 65423.387 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: fusion protein of T-complex protein 1 subunit gamma,rep-His-CBP and T-complex protein 1 subunit gamma Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: CCT3, BIN2, TCP3, YJL014W, J1336 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39077 #6: Protein | Mass: 59802.438 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: CCT7 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P42943 #7: Protein | Mass: 61735.102 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: CCT8, YJL008C, J1374 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P47079 #9: Protein | Mass: 59997.559 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: CCT6, TCP20, TCP6, YDR188W, YD9395.21 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39079 |
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-Protein , 2 types, 2 molecules Tp
#8: Protein | Mass: 50967.457 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: TUB2, GI527_G0002040 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PXT5 |
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#10: Protein | Mass: 32836.270 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: PLP2, VIAF1, YOR281C / Production host: Escherichia coli (E. coli) / References: UniProt: Q12017 |
-Non-polymers , 5 types, 61 molecules
#11: Chemical | ChemComp-ADP / #12: Chemical | ChemComp-MG / #13: Chemical | ChemComp-AF3 / #14: Chemical | ChemComp-GTP / | #15: 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 |
-Sample preparation
Component |
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Source (natural) |
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Source (recombinant) | Organism: Eschericia 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: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 38 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28063 / Symmetry type: POINT |