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Yorodumi- PDB-7lup: Human TRiC/CCT complex with reovirus outer capsid protein sigma-3 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lup | |||||||||||||||||||||||||||||||||
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Title | Human TRiC/CCT complex with reovirus outer capsid protein sigma-3 | |||||||||||||||||||||||||||||||||
Components |
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Keywords | CHAPERONE / tric / cct / reovirus capsid / sigma 3 | |||||||||||||||||||||||||||||||||
Function / homology | Function and homology information zona pellucida receptor complex / scaRNA localization to Cajal body / symbiont-mediated suppression of host PKR/eIFalpha signaling / chaperone mediated protein folding independent of cofactor / viral outer capsid / 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 ...zona pellucida receptor complex / scaRNA localization to Cajal body / symbiont-mediated suppression of host PKR/eIFalpha signaling / chaperone mediated protein folding independent of cofactor / viral outer capsid / 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 / protein serine/threonine kinase inhibitor activity / 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 / : / viral life cycle / 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 / regulation of translation / cell body / secretory granule lumen / microtubule / ficolin-1-rich granule lumen / host cell cytoplasm / cytoskeleton / protein stabilization / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / cadherin binding / virus-mediated perturbation of host defense response / centrosome / ubiquitin protein ligase binding / host cell nucleus / Neutrophil degranulation / structural molecule activity / Golgi apparatus / ATP hydrolysis activity / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||||||||||||||||||||||||||
Biological species | Homo sapiens (human) Reovirus type 3 | |||||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.2 Å | |||||||||||||||||||||||||||||||||
Authors | Knowlton, J.J. / Gestaut, D. / Ma, B. / Taylor, G. / Seven, A.B. / Leitner, A. / Wilson, G.J. / Shanker, S. / Yates, N.A. / Prasad, B.V.V. ...Knowlton, J.J. / Gestaut, D. / Ma, B. / Taylor, G. / Seven, A.B. / Leitner, A. / Wilson, G.J. / Shanker, S. / Yates, N.A. / Prasad, B.V.V. / Aebersold, R. / Chiu, W. / Frydman, J. / Dermody, T.S. | |||||||||||||||||||||||||||||||||
Funding support | United States, European Union, 10items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2021 Title: Structural and functional dissection of reovirus capsid folding and assembly by the prefoldin-TRiC/CCT chaperone network. Authors: Jonathan J Knowlton / Daniel Gestaut / Boxue Ma / Gwen Taylor / Alpay Burak Seven / Alexander Leitner / Gregory J Wilson / Sreejesh Shanker / Nathan A Yates / B V Venkataram Prasad / Ruedi ...Authors: Jonathan J Knowlton / Daniel Gestaut / Boxue Ma / Gwen Taylor / Alpay Burak Seven / Alexander Leitner / Gregory J Wilson / Sreejesh Shanker / Nathan A Yates / B V Venkataram Prasad / Ruedi Aebersold / Wah Chiu / Judith Frydman / Terence S Dermody / Abstract: Intracellular protein homeostasis is maintained by a network of chaperones that function to fold proteins into their native conformation. The eukaryotic TRiC chaperonin (TCP1-ring complex, also ...Intracellular protein homeostasis is maintained by a network of chaperones that function to fold proteins into their native conformation. The eukaryotic TRiC chaperonin (TCP1-ring complex, also called CCT for cytosolic chaperonin containing TCP1) facilitates folding of a subset of proteins with folding constraints such as complex topologies. To better understand the mechanism of TRiC folding, we investigated the biogenesis of an obligate TRiC substrate, the reovirus σ3 capsid protein. We discovered that the σ3 protein interacts with a network of chaperones, including TRiC and prefoldin. Using a combination of cryoelectron microscopy, cross-linking mass spectrometry, and biochemical approaches, we establish functions for TRiC and prefoldin in folding σ3 and promoting its assembly into higher-order oligomers. These studies illuminate the molecular dynamics of σ3 folding and establish a biological function for TRiC in virus assembly. In addition, our findings provide structural and functional insight into the mechanism by which TRiC and prefoldin participate in the assembly of protein complexes. | |||||||||||||||||||||||||||||||||
History |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7lup.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7lup.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 7lup.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lup_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7lup_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7lup_validation.xml.gz | 276.3 KB | Display | |
Data in CIF | 7lup_validation.cif.gz | 412.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/7lup ftp://data.pdbj.org/pub/pdb/validation_reports/lu/7lup | HTTPS FTP |
-Related structure data
Related structure data | 23526MC 7lumC 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 LDMENFHPKCJBIAOG
#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: Insect cell expression vector pTIE1 (others) References: UniProt: P48643 #2: Protein | Mass: 57567.141 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCT2, 99D8.1, CCTB Production host: Insect cell expression vector pTIE1 (others) References: UniProt: P78371 #3: Protein | Mass: 57996.113 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCT4, CCTD, SRB Production host: Insect cell expression vector pTIE1 (others) References: UniProt: P50991 #4: Protein | Mass: 60613.855 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCT3, CCTG, TRIC5 Production host: Insect cell expression vector pTIE1 (others) References: UniProt: P49368 #5: Protein | Mass: 59443.535 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCT7, CCTH, NIP7-1 Production host: Insect cell expression vector pTIE1 (others) References: UniProt: Q99832 #6: Protein | Mass: 59691.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCT8, C21orf112, CCTQ, KIAA0002 Production host: Insect cell expression vector pTIE1 (others) References: UniProt: P50990 #7: Protein | Mass: 58106.086 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCT6A, CCT6, CCTZ Production host: Insect cell expression vector pTIE1 (others) References: UniProt: P40227 #8: Protein | Mass: 60418.477 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TCP1, CCT1, CCTA Production host: Insect cell expression vector pTIE1 (others) References: UniProt: P17987 |
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-Protein , 1 types, 1 molecules Q
#9: Protein | Mass: 41168.121 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Reovirus type 3 (strain Dearing) / Strain: Dearing / Gene: S4 Production host: Insect cell expression vector pTIE1 (others) References: UniProt: P03527 |
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-Non-polymers , 2 types, 421 molecules
#10: Chemical | ChemComp-ZN / |
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#11: Water | ChemComp-HOH / |
-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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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: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 36 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26000 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 87.21 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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