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- PDB-7lum: Human TRiC in ATP/AlFx closed state -

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Basic information

Entry
Database: PDB / ID: 7lum
TitleHuman TRiC in ATP/AlFx closed state
Components(T-complex protein 1 subunit ...) x 8
KeywordsCHAPERONE / tric / cct
Function / homology
Function and homology information


zona pellucida receptor complex / scaRNA localization to Cajal body / 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 ...zona pellucida receptor complex / scaRNA localization to Cajal body / 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 / 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 / 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 / ubiquitin protein ligase binding / Neutrophil degranulation / Golgi apparatus / ATP hydrolysis activity / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / cytosol / cytoplasm
Similarity search - Function
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. ...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
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 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


Theoretical massNumber of molelcules
Total (without water)947,17316
Polymers947,17316
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "I"
d_2ens_1chain "A"
d_1ens_2chain "J"
d_2ens_2chain "B"
d_1ens_3chain "C"
d_2ens_3chain "K"
d_1ens_4chain "D"
d_2ens_4chain "L"
d_1ens_5chain "M"
d_2ens_5chain "E"
d_1ens_6chain "F"
d_2ens_6chain "N"
d_1ens_7chain "G"
d_2ens_7chain "O"
d_1ens_8chain "H"
d_2ens_8chain "P"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALASERM1 - 525
d_21ens_1ALASERN1 - 525
d_11ens_2PROPROK1 - 524
d_21ens_2PROPROL1 - 524
d_11ens_3METPROJ1 - 522
d_21ens_3METPROI1 - 522
d_11ens_4TYRGLUB1 - 527
d_21ens_4TYRGLUA1 - 527
d_11ens_5VALARGC1 - 518
d_21ens_5VALARGD1 - 518
d_11ens_6GLYARGF1 - 518
d_21ens_6GLYARGE1 - 518
d_11ens_7LEUGLUP1 - 532
d_21ens_7LEUGLUO1 - 532
d_11ens_8LEULYSG1 - 521
d_21ens_8LEULYSH1 - 521

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4
ens_5
ens_6
ens_7
ens_8

NCS oper:
IDCodeMatrixVector
1given(-0.999855906979, 0.015348136154, -0.0072525854642), (-0.0151895178438, -0.999654707432, -0.021441652374), (-0.00757917060034, -0.0213283995052, 0.999743794953)189.949824147, 174.487150149, 2.70435427908
2given(-0.999962888328, 0.00861511311068, -4.234066242E-5), (-0.00861016268444, -0.999532474172, -0.0293376579593), (-0.000295068108788, -0.0293362046297, 0.999569557376)189.10415237, 174.45867627, 2.39327875529
3given(-0.9998293494, 0.00270685697703, 0.0182741622023), (-0.00309960904829, -0.999764081936, -0.0214982067697), (0.0182116584264, -0.0215511808463, 0.999601861794)187.910802219, 173.832933943, -0.587540441908
4given(-0.999992641732, 5.3031237298E-7, 0.00383620659039), (-0.000121062014868, -0.999506283377, -0.0314193385242), (0.00383429592937, -0.0314195717512, 0.999498928807)189.533773354, 174.169660082, 2.41930394195
5given(-0.999949789168, -0.00223206707799, 0.00976918724007), (0.00196439575911, -0.999624702483, -0.027323896762), (0.00982650965877, -0.0273033342564, 0.999578895159)189.294537362, 173.572847249, 1.3652965805
6given(-0.999890590473, 0.0112499786382, -0.00960442942081), (-0.0109208992463, -0.999373865381, -0.0336542887824), (-0.00997702578494, -0.0335457176765, 0.999387384242)189.048195449, 174.904822241, 3.40214955133
7given(-0.999955998729, 0.00721801265086, -0.00599173598751), (-0.00706122999283, -0.999642503495, -0.0257876760846), (-0.00617572973505, -0.0257442323682, 0.999649486001)189.473122719, 174.204359681, 2.43868329288
8given(-0.999978474893, -0.00147171355645, 0.0063940448821), (0.00127397164815, -0.999524117354, -0.030820704479), (0.0064363613157, -0.0308118952282, 0.999504477411)189.142955732, 174.183463393, 2.33355245353

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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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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

ComponentName: human TRiC/CCT complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 1 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Insect cell expression vector pTIE1 (others)
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: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 334000 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 90.92 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006564728
ELECTRON MICROSCOPYf_angle_d0.818987340
ELECTRON MICROSCOPYf_chiral_restr0.046610456
ELECTRON MICROSCOPYf_plane_restr0.004611232
ELECTRON MICROSCOPYf_dihedral_angle_d32.64198906
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2MELECTRON MICROSCOPYNCS constraints0.000701961836842
ens_2d_2KELECTRON MICROSCOPYNCS constraints0.0502597643658
ens_3d_2JELECTRON MICROSCOPYNCS constraints0.050123121393
ens_4d_2BELECTRON MICROSCOPYNCS constraints0.00071364804617
ens_5d_2CELECTRON MICROSCOPYNCS constraints0.00070939335197
ens_6d_2FELECTRON MICROSCOPYNCS constraints0.000700398901969
ens_7d_2PELECTRON MICROSCOPYNCS constraints0.0007104177652
ens_8d_2GELECTRON MICROSCOPYNCS constraints0.000701809382771

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