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- PDB-6nrc: hTRiC-hPFD Class3 -

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Basic information

Entry
Database: PDB / ID: 6nrc
TitlehTRiC-hPFD Class3
Components
  • (Prefoldin subunit ...) x 6
  • (T-complex protein 1 subunit ...) x 8
KeywordsCHAPERONE / TRiC/CCT / PFD / CryoEM / Molecular Chaperone / Protein folding
Function / homology
Function and homology information


RNA polymerase I assembly / RNA polymerase III assembly / prefoldin complex / positive regulation of cytoskeleton organization / 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 / RNA polymerase II core complex assembly ...RNA polymerase I assembly / RNA polymerase III assembly / prefoldin complex / positive regulation of cytoskeleton organization / 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 / RNA polymerase II core complex assembly / tubulin complex assembly / chaperonin-containing T-complex / RPAP3/R2TP/prefoldin-like complex / BBSome-mediated cargo-targeting to cilium / binding of sperm to zona pellucida / positive regulation of telomerase RNA localization to Cajal body / Folding of actin by CCT/TriC / Formation of tubulin folding intermediates by CCT/TriC / Prefoldin mediated transfer of substrate to CCT/TriC / negative regulation of amyloid fibril formation / protein folding chaperone complex / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / WD40-repeat domain binding / pericentriolar material / beta-tubulin binding / : / Association of TriC/CCT with target proteins during biosynthesis / microtubule-based process / chaperone-mediated protein complex assembly / RHOBTB2 GTPase cycle / heterochromatin / chaperone-mediated protein folding / protein folding chaperone / positive regulation of telomere maintenance via telomerase / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / tubulin binding / acrosomal vesicle / cell projection / mRNA 3'-UTR binding / ATP-dependent protein folding chaperone / response to virus / negative regulation of canonical Wnt signaling pathway / cilium / mRNA 5'-UTR binding / transcription corepressor activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / azurophil granule lumen / G-protein beta-subunit binding / unfolded protein binding / melanosome / protein folding / retina development in camera-type eye / amyloid-beta binding / protein-folding chaperone binding / cell body / secretory granule lumen / ficolin-1-rich granule lumen / microtubule / cytoskeleton / protein stabilization / cadherin binding / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / regulation of DNA-templated transcription / Golgi apparatus / ATP hydrolysis activity / mitochondrion / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Prefoldin subunit 3 / Prefoldin, subunit 4 / Prefoldin subunit 2 / Prefoldin beta-like / Prefoldin alpha-like / Prefoldin alpha subunit, archaea-type / Prefoldin subunit / Prefoldin subunit / Prefoldin / T-complex protein 1, alpha subunit ...Prefoldin subunit 3 / Prefoldin, subunit 4 / Prefoldin subunit 2 / Prefoldin beta-like / Prefoldin alpha-like / Prefoldin alpha subunit, archaea-type / Prefoldin subunit / Prefoldin subunit / Prefoldin / 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
Prefoldin subunit 6 / Prefoldin subunit 1 / 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 / Prefoldin subunit 3 / T-complex protein 1 subunit beta ...Prefoldin subunit 6 / Prefoldin subunit 1 / 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 / Prefoldin subunit 3 / T-complex protein 1 subunit beta / Prefoldin subunit 5 / T-complex protein 1 subunit eta / Prefoldin subunit 4 / Prefoldin subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.3 Å
AuthorsGestaut, D. / Roh, S.H. / Ma, B. / Pintilie, G. / Joachimiak, L.A. / Leitner, A. / Walzthoeni, T. / Aebersold, R. / Chiu, W. / Frydman, J.
Funding support United States, European Union, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM074074 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)F32GM103124 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)R01GM079429 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)P01NS092525 United States
European Research Council (ERC)AdvG #233226European Union
European Research Council (ERC)AdvG #670821European Union
CitationJournal: Cell / Year: 2019
Title: The Chaperonin TRiC/CCT Associates with Prefoldin through a Conserved Electrostatic Interface Essential for Cellular Proteostasis.
Authors: Daniel Gestaut / Soung Hun Roh / Boxue Ma / Grigore Pintilie / Lukasz A Joachimiak / Alexander Leitner / Thomas Walzthoeni / Ruedi Aebersold / Wah Chiu / Judith Frydman /
Abstract: Maintaining proteostasis in eukaryotic protein folding involves cooperation of distinct chaperone systems. To understand how the essential ring-shaped chaperonin TRiC/CCT cooperates with the ...Maintaining proteostasis in eukaryotic protein folding involves cooperation of distinct chaperone systems. To understand how the essential ring-shaped chaperonin TRiC/CCT cooperates with the chaperone prefoldin/GIMc (PFD), we integrate cryoelectron microscopy (cryo-EM), crosslinking-mass-spectrometry and biochemical and cellular approaches to elucidate the structural and functional interplay between TRiC/CCT and PFD. We find these hetero-oligomeric chaperones associate in a defined architecture, through a conserved interface of electrostatic contacts that serves as a pivot point for a TRiC-PFD conformational cycle. PFD alternates between an open "latched" conformation and a closed "engaged" conformation that aligns the PFD-TRiC substrate binding chambers. PFD can act after TRiC bound its substrates to enhance the rate and yield of the folding reaction, suppressing non-productive reaction cycles. Disrupting the TRiC-PFD interaction in vivo is strongly deleterious, leading to accumulation of amyloid aggregates. The supra-chaperone assembly formed by PFD and TRiC is essential to prevent toxic conformations and ensure effective cellular proteostasis.
History
DepositionJan 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.2Mar 20, 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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Assembly

Deposited unit
1: Prefoldin subunit 1
2: Prefoldin subunit 2
3: Prefoldin subunit 3
4: Prefoldin subunit 4
5: Prefoldin subunit 5
6: Prefoldin subunit 6
A: T-complex protein 1 subunit alpha
B: T-complex protein 1 subunit beta
C: T-complex protein 1 subunit gamma
D: T-complex protein 1 subunit delta
E: T-complex protein 1 subunit epsilon
F: T-complex protein 1 subunit zeta
G: T-complex protein 1 subunit eta
H: T-complex protein 1 subunit theta
I: T-complex protein 1 subunit alpha
J: T-complex protein 1 subunit beta
K: T-complex protein 1 subunit gamma
L: T-complex protein 1 subunit delta
M: T-complex protein 1 subunit epsilon
N: T-complex protein 1 subunit zeta
O: T-complex protein 1 subunit eta
P: T-complex protein 1 subunit theta


Theoretical massNumber of molelcules
Total (without water)981,45622
Polymers981,45622
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area81700 Å2
ΔGint-327 kcal/mol
Surface area316660 Å2

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Components

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Prefoldin subunit ... , 6 types, 6 molecules 123456

#1: Protein Prefoldin subunit 1


Mass: 12522.427 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PFDN1, PFD1
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: O60925
#2: Protein Prefoldin subunit 2


Mass: 11862.538 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PFDN2, PFD2, HSPC231
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q9UHV9
#3: Protein Prefoldin subunit 3 / HIBBJ46 / von Hippel-Lindau-binding protein 1 / VHL-binding protein 1


Mass: 15558.005 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VBP1, PFDN3
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: P61758
#4: Protein Prefoldin subunit 4 / Protein C-1


Mass: 12142.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PFDN4, PFD4
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q9NQP4
#5: Protein Prefoldin subunit 5 / Myc modulator 1 / c-Myc-binding protein Mm-1


Mass: 14579.903 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PFDN5, MM1, PFD5
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q99471
#6: Protein Prefoldin subunit 6 / Protein Ke2


Mass: 11775.323 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PFDN6, HKE2, PFD6
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: O15212

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

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


Mass: 58061.055 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
#8: Protein T-complex protein 1 subunit beta / TCP-1-beta / CCT-beta


Mass: 54736.742 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
#9: Protein T-complex protein 1 subunit gamma / TCP-1-gamma / CCT-gamma / hTRiC5


Mass: 57165.945 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
#10: Protein T-complex protein 1 subunit delta / TCP-1-delta / CCT-delta / Stimulator of TAR RNA-binding


Mass: 55636.500 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
#11: Protein T-complex protein 1 subunit epsilon / TCP-1-epsilon / CCT-epsilon


Mass: 56989.797 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
#12: Protein T-complex protein 1 subunit zeta / TCP-1-zeta / Acute morphine dependence-related protein 2 / CCT-zeta-1 / HTR3 / Tcp20


Mass: 56445.008 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
#13: Protein T-complex protein 1 subunit eta / TCP-1-eta / CCT-eta / HIV-1 Nef-interacting protein


Mass: 56369.867 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
#14: 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: 56102.406 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

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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
IDNameTypeDetailsEntity IDParent-IDSource
1hTRiC-hPFDCOMPLEXcomplex of hTRiC-hPFDall0RECOMBINANT
2hTRiCCOMPLEX#7-#141RECOMBINANT
3hPFDCOMPLEX#1-#61RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
22Homo sapiens (human)9606
33Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
11Insect cell expression vector pTIE1 (others)266783
22Insect cell expression vector pTIE1 (others)266783
33Insect cell expression vector pTIE1 (others)266783
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 1 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 8.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9580 / Symmetry type: POINT

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