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- PDB-7lup: Human TRiC/CCT complex with reovirus outer capsid protein sigma-3 -

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Basic information

Entry
Database: PDB / ID: 7lup
TitleHuman TRiC/CCT complex with reovirus outer capsid protein sigma-3
Components
  • (T-complex protein 1 subunit ...) x 8
  • Outer capsid protein sigma-3
KeywordsCHAPERONE / tric / cct / reovirus capsid / sigma 3
Function / homology
Function and homology information


symbiont-mediated suppression of host PKR/eIFalpha signaling / zona pellucida receptor complex / scaRNA localization to Cajal body / viral outer capsid / positive regulation of protein localization to Cajal body / tubulin complex assembly / chaperone mediated protein folding independent of cofactor / positive regulation of establishment of protein localization to telomere / BBSome-mediated cargo-targeting to cilium / chaperonin-containing T-complex ...symbiont-mediated suppression of host PKR/eIFalpha signaling / zona pellucida receptor complex / scaRNA localization to Cajal body / viral outer capsid / positive regulation of protein localization to Cajal body / tubulin complex assembly / chaperone mediated protein folding independent of cofactor / positive regulation of establishment of protein localization to telomere / BBSome-mediated cargo-targeting to cilium / chaperonin-containing T-complex / Folding of actin by CCT/TriC / positive regulation of telomerase RNA localization to Cajal body / Formation of tubulin folding intermediates by CCT/TriC / binding of sperm to zona pellucida / Prefoldin mediated transfer of substrate to CCT/TriC / protein serine/threonine kinase inhibitor activity / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / WD40-repeat domain binding / beta-tubulin binding / pericentriolar material / Association of TriC/CCT with target proteins during biosynthesis / chaperone-mediated protein complex assembly / heterochromatin / RHOBTB2 GTPase cycle / chaperone-mediated protein folding / protein folding chaperone / viral life cycle / positive regulation of telomerase activity / positive regulation of telomere maintenance via telomerase / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / acrosomal vesicle / mRNA 3'-UTR binding / cell projection / 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 / melanosome / unfolded protein binding / protein folding / cell body / secretory granule lumen / microtubule / ficolin-1-rich granule lumen / protein stabilization / cytoskeleton / cadherin binding / centrosome / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ubiquitin protein ligase binding / Neutrophil degranulation / structural molecule activity / Golgi apparatus / ATP hydrolysis activity / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Reovirus, outer capsid sigma 3 / Reovirus, outer capsid sigma-3 domain superfamily / Reovirus outer capsid protein, Sigma 3 / T-complex protein 1, alpha subunit / T-complex protein 1, eta subunit / T-complex protein 1, theta subunit / T-complex protein 1, zeta subunit / T-complex protein 1, delta subunit / T-complex protein 1, gamma subunit / T-complex protein 1, epsilon subunit ...Reovirus, outer capsid sigma 3 / Reovirus, outer capsid sigma-3 domain superfamily / Reovirus outer capsid protein, Sigma 3 / T-complex protein 1, alpha subunit / T-complex protein 1, eta subunit / T-complex protein 1, theta subunit / T-complex protein 1, zeta subunit / T-complex protein 1, delta subunit / T-complex protein 1, gamma subunit / T-complex protein 1, epsilon subunit / T-complex protein 1, beta subunit / Chaperonins TCP-1 signature 1. / Chaperonins TCP-1 signature 2. / Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 3. / Chaperone tailless complex polypeptide 1 (TCP-1) / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family
Similarity search - Domain/homology
Outer capsid protein sigma-3 / T-complex protein 1 subunit alpha / T-complex protein 1 subunit zeta / T-complex protein 1 subunit epsilon / T-complex protein 1 subunit gamma / T-complex protein 1 subunit theta / T-complex protein 1 subunit delta / T-complex protein 1 subunit beta / T-complex protein 1 subunit eta
Similarity search - Component
Biological speciesHomo sapiens (human)
Reovirus type 3
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.2 Å
AuthorsKnowlton, 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
OrganizationGrant numberCountry
Robert A. Welch FoundationQ1279 United States
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)UL1TR000445 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)P41GM103832 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)P01NS092525 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM007347 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM074074 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103124 United States
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)UL1TR000445 United States
European Research Council (ERC)AdvG 233226European Union
European Research Council (ERC)AdvG 670821European Union
CitationJournal: 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
DepositionFeb 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
L: T-complex protein 1 subunit epsilon
D: T-complex protein 1 subunit epsilon
M: T-complex protein 1 subunit beta
E: T-complex protein 1 subunit beta
N: T-complex protein 1 subunit delta
F: T-complex protein 1 subunit delta
H: T-complex protein 1 subunit gamma
P: T-complex protein 1 subunit gamma
K: T-complex protein 1 subunit eta
C: T-complex protein 1 subunit eta
J: T-complex protein 1 subunit theta
B: T-complex protein 1 subunit theta
I: T-complex protein 1 subunit zeta
A: T-complex protein 1 subunit zeta
O: T-complex protein 1 subunit alpha
G: T-complex protein 1 subunit alpha
Q: Outer capsid protein sigma-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)988,40718
Polymers988,34117
Non-polymers651
Water7,566420
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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T-complex protein 1 subunit ... , 8 types, 16 molecules LDMENFHPKCJBIAOG

#1: Protein T-complex protein 1 subunit epsilon / TCP-1-epsilon / CCT-epsilon


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 T-complex protein 1 subunit beta / TCP-1-beta / CCT-beta


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 T-complex protein 1 subunit delta / TCP-1-delta / CCT-delta / Stimulator of TAR RNA-binding


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 T-complex protein 1 subunit gamma / TCP-1-gamma / CCT-gamma / hTRiC5


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 T-complex protein 1 subunit eta / TCP-1-eta / CCT-eta / HIV-1 Nef-interacting 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 T-complex protein 1 subunit theta / TCP-1-theta / CCT-theta / Chaperonin containing T-complex polypeptide 1 subunit 8 / Renal carcinoma ...TCP-1-theta / CCT-theta / Chaperonin containing T-complex polypeptide 1 subunit 8 / Renal carcinoma antigen NY-REN-15


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 T-complex protein 1 subunit zeta / TCP-1-zeta / Acute morphine dependence-related protein 2 / CCT-zeta-1 / HTR3 / Tcp20


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 T-complex protein 1 subunit alpha / TCP-1-alpha / CCT-alpha


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 Outer capsid protein sigma-3 / Sigma3


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 / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 420 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1human TRiC/CCT complex with reovirus outer capsid protein sigma-3COMPLEX#1-#90MULTIPLE SOURCES
2human TRiC/CCT complexCOMPLEX#1-#81RECOMBINANT
3reovirus outer capsid protein sigma-3COMPLEX#91RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
111 MDaNO
211 MDaNO
3141 kDa/nmNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Mammalian orthoreovirus 3 Dearing10886
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Insect cell expression vector pTIE1 (others)266783
23Insect cell expression vector pTIE1 (others)266783
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 36 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26000 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 87.21 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006267683
ELECTRON MICROSCOPYf_angle_d0.861591345
ELECTRON MICROSCOPYf_chiral_restr0.045310886
ELECTRON MICROSCOPYf_plane_restr0.005711752
ELECTRON MICROSCOPYf_dihedral_angle_d26.079325672

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