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- PDB-9umt: TRiC_HDAC1_close_state -

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Basic information

Entry
Database: PDB / ID: 9umt
TitleTRiC_HDAC1_close_state
Components(T-complex protein 1 subunit ...) x 8
KeywordsCHAPERONE / TRiC complex
Function / homology
Function and homology information


positive regulation of protein localization to Cajal body / zona pellucida receptor complex / positive regulation of establishment of protein localization to telomere / scaRNA localization to Cajal body / positive regulation of telomerase RNA localization to Cajal body / chaperonin-containing T-complex / BBSome-mediated cargo-targeting to cilium / tubulin complex assembly / Formation of tubulin folding intermediates by CCT/TriC / binding of sperm to zona pellucida ...positive regulation of protein localization to Cajal body / zona pellucida receptor complex / positive regulation of establishment of protein localization to telomere / scaRNA localization to Cajal body / positive regulation of telomerase RNA localization to Cajal body / chaperonin-containing T-complex / BBSome-mediated cargo-targeting to cilium / tubulin complex assembly / Formation of tubulin folding intermediates by CCT/TriC / binding of sperm to zona pellucida / Folding of actin by CCT/TriC / Prefoldin mediated transfer of substrate to CCT/TriC / RHOBTB1 GTPase cycle / WD40-repeat domain binding / pericentriolar material / Association of TriC/CCT with target proteins during biosynthesis / sperm head-tail coupling apparatus / chaperone-mediated protein complex assembly / RHOBTB2 GTPase cycle / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / beta-tubulin binding / heterochromatin / positive regulation of telomere maintenance via telomerase / protein folding chaperone / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / acrosomal vesicle / mRNA 3'-UTR binding / ATP-dependent protein folding chaperone / mRNA 5'-UTR binding / response to virus / azurophil granule lumen / : / melanosome / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / G-protein beta-subunit binding / protein folding / cell body / sperm midpiece / secretory granule lumen / ficolin-1-rich granule lumen / cytoskeleton / microtubule / protein stabilization / cadherin binding / Neutrophil degranulation / ubiquitin protein ligase binding / centrosome / Golgi apparatus / ATP hydrolysis activity / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / cytoplasm / cytosol
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. ...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
ADENOSINE-5'-DIPHOSPHATE / ALUMINUM FLUORIDE / 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: 3.64 Å
AuthorsLi, Z.L. / Cong, Y.C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: TRiC-assisted folding of class I HDAC family proteins regulated by distinct co-chaperone and cofactor networks
Authors: Li, Z.L. / Cong, Y.C.
History
DepositionApr 23, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
F: T-complex protein 1 subunit alpha
A: T-complex protein 1 subunit beta
C: T-complex protein 1 subunit gamma
B: T-complex protein 1 subunit delta
G: T-complex protein 1 subunit epsilon
H: T-complex protein 1 subunit zeta
D: T-complex protein 1 subunit eta
E: T-complex protein 1 subunit theta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)464,35432
Polymers460,0708
Non-polymers4,28424
Water1448
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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T-complex protein 1 subunit ... , 8 types, 8 molecules FACBGHDE

#1: Protein T-complex protein 1 subunit alpha / TCP-1-alpha / CCT-alpha / Chaperonin containing T-complex polypeptide 1 subunit 1


Mass: 57840.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCP1, CCT1, CCTA / Production host: Homo sapiens (human) / References: UniProt: P17987
#2: Protein T-complex protein 1 subunit beta / TCP-1-beta / CCT-beta / Chaperonin containing T-complex polypeptide 1 subunit 2


Mass: 56490.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCT2, 99D8.1, CCTB / Production host: Homo sapiens (human) / References: UniProt: P78371
#3: Protein T-complex protein 1 subunit gamma / TCP-1-gamma / CCT-gamma / Chaperonin containing T-complex polypeptide 1 subunit 3 / hTRiC5


Mass: 58585.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCT3, CCTG, TRIC5 / Production host: Homo sapiens (human) / References: UniProt: P49368
#4: Protein T-complex protein 1 subunit delta / TCP-1-delta / CCT-delta / Chaperonin containing T-complex polypeptide 1 subunit 4 / Stimulator of ...TCP-1-delta / CCT-delta / Chaperonin containing T-complex polypeptide 1 subunit 4 / Stimulator of TAR RNA-binding


Mass: 55998.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCT4, CCTD, SRB / Production host: Homo sapiens (human) / References: UniProt: P50991
#5: Protein T-complex protein 1 subunit epsilon / TCP-1-epsilon / CCT-epsilon / Chaperonin containing T-complex polypeptide 1 subunit 5


Mass: 58696.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCT5, CCTE, KIAA0098 / Production host: Homo sapiens (human) / References: UniProt: P48643
#6: Protein T-complex protein 1 subunit zeta / TCP-1-zeta / Acute morphine dependence-related protein 2 / CCT-zeta-1 / Chaperonin containing T- ...TCP-1-zeta / Acute morphine dependence-related protein 2 / CCT-zeta-1 / Chaperonin containing T-complex polypeptide 1 subunit 6A / HTR3 / Tcp20


Mass: 57501.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCT6A, CCT6, CCTZ / Production host: Homo sapiens (human) / References: UniProt: P40227
#7: Protein T-complex protein 1 subunit eta / TCP-1-eta / CCT-eta


Mass: 57336.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q53HV2
#8: 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: 57619.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCT8, C21orf112, CCTQ, KIAA0002 / Production host: Homo sapiens (human) / References: UniProt: P50990

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Non-polymers , 4 types, 32 molecules

#9: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#10: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical
ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: AlF3 / Feature type: SUBJECT OF INVESTIGATION
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: TRiC complex eith HDAC3 / Type: COMPLEX / Entity ID: #1-#8 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 25000 nm / Nominal defocus min: 8000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 130389 / Symmetry type: POINT
RefinementHighest resolution: 3.64 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00632776
ELECTRON MICROSCOPYf_angle_d1.27544265
ELECTRON MICROSCOPYf_dihedral_angle_d8.0714564
ELECTRON MICROSCOPYf_chiral_restr0.0585287
ELECTRON MICROSCOPYf_plane_restr0.0085647

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