9S72 | pdb_00009s72

Human CCT in Closed Conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.71 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history

Literature

CryoEM Strategies for Elucidating the Closed State Architecture of CCT.

Gutierrez-Seijo, J.Cuervo, A.Pipaon, S.Gil-Cantero, D.Majano, C.Santiago, C.Valpuesta, J.M.Cuellar, J.

(2026) Methods Mol Biol 3070: 263-282

  • DOI: https://doi.org/10.1007/978-1-0716-5515-3_15
  • Primary Citation Related Structures: 
    9S72

  • PubMed Abstract: 

    Cryo-electron microscopy (CryoEM) has emerged as a state-of-the-art technique in structural biology, thanks to advances in sample preparation, high-voltage electron microscopy, direct electron detectors, and sophisticated image processing software. In this study, we investigate the eukaryotic chaperonin CCT, a ~1 MDa hetero-oligomeric complex essential for the folding of key substrates such as actin, tubulin, and WD40 family members. While several open-state structures of CCT have been resolved, the highest-resolution reconstructions have been obtained in the closed state. This is primarily due to the increased structural rigidity of the complex when its apical domains become immobilized in this conformation. However, the pseudo-symmetric arrangement of subunits in the closed state poses challenges for subunit identification. Here, we present a workflow for obtaining a high-resolution CryoEM structure of closed CCT, achieved without the use of nanobodies, substrates, or any tools designed to increase CCT asymmetry. Our results demonstrate that subunit assignment and atomic modeling are achievable by exploiting subunit-intrinsic structural features alone.


  • Organizational Affiliation
    • Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain.

Macromolecule Content 

  • Total Structure Weight: 955.74 kDa 
  • Atom Count: 64,888 
  • Modeled Residue Count: 8,428 
  • Deposited Residue Count: 8,676 
  • Unique protein chains: 8

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit alphaA,
I [auth a]
556Homo sapiensMutation(s): 0 
EC: 3.6.1
UniProt & NIH Common Fund Data Resources
Find proteins for P17987 (Homo sapiens)
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PHAROS:  P17987
GTEx:  ENSG00000120438 
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UniProt GroupP17987
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit betaB [auth b],
J [auth B]
535Homo sapiensMutation(s): 0 
EC: 3.6.1
UniProt & NIH Common Fund Data Resources
Find proteins for P78371 (Homo sapiens)
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PHAROS:  P78371
GTEx:  ENSG00000166226 
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UniProt GroupP78371
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit gammaC,
K [auth c]
545Homo sapiensMutation(s): 0 
EC: 3.6.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49368 (Homo sapiens)
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PHAROS:  P49368
GTEx:  ENSG00000163468 
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UniProt GroupP49368
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit deltaD,
L [auth d]
539Homo sapiensMutation(s): 0 
EC: 3.6.1
UniProt & NIH Common Fund Data Resources
Find proteins for P50991 (Homo sapiens)
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GTEx:  ENSG00000115484 
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit epsilonE [auth e],
M [auth E]
541Homo sapiensMutation(s): 0 
EC: 3.6.1
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Find proteins for P48643 (Homo sapiens)
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GTEx:  ENSG00000150753 
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UniProt GroupP48643
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit zetaF,
N [auth f]
531Homo sapiensMutation(s): 0 
EC: 3.6.1
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Find proteins for P40227 (Homo sapiens)
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GTEx:  ENSG00000146731 
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit etaG [auth g],
O [auth G]
543Homo sapiensMutation(s): 0 
EC: 3.6.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99832 (Homo sapiens)
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PHAROS:  Q99832
GTEx:  ENSG00000135624 
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UniProt GroupQ99832
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit thetaH [auth h],
P [auth H]
548Homo sapiensMutation(s): 0 
EC: 3.6.1
UniProt & NIH Common Fund Data Resources
Find proteins for P50990 (Homo sapiens)
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GTEx:  ENSG00000156261 
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
(Subject of Investigation/LOI)

Query on ADP



Download:Ideal Coordinates CCD File
AB [auth E]
CA [auth e]
DB [auth f]
FA [auth F]
GB [auth G]
AB [auth E],
CA [auth e],
DB [auth f],
FA [auth F],
GB [auth G],
IA [auth g],
JB [auth H],
LA [auth h],
OA [auth a],
Q [auth A],
RA [auth B],
T [auth b],
UA [auth c],
W [auth C],
XA [auth d],
Z [auth D]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
AF3
(Subject of Investigation/LOI)

Query on AF3



Download:Ideal Coordinates CCD File
BA [auth D]
CB [auth E]
EA [auth e]
FB [auth f]
HA [auth F]
BA [auth D],
CB [auth E],
EA [auth e],
FB [auth f],
HA [auth F],
IB [auth G],
KA [auth g],
LB [auth H],
NA [auth h],
QA [auth a],
S [auth A],
TA [auth B],
V [auth b],
WA [auth c],
Y [auth C],
ZA [auth d]
ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-UHFFFAOYSA-K
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
AA [auth D]
BB [auth E]
DA [auth e]
EB [auth f]
GA [auth F]
AA [auth D],
BB [auth E],
DA [auth e],
EB [auth f],
GA [auth F],
HB [auth G],
JA [auth g],
KB [auth H],
MA [auth h],
PA [auth a],
R [auth A],
SA [auth B],
U [auth b],
VA [auth c],
X [auth C],
YA [auth d]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.71 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.0
RECONSTRUCTIONDeepEMhancer0.17
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainPID2022-137175NB-I00

Revision History  (Full details and data files)

  • Version 1.0: 2026-09-16
    Type: Initial release