9E2S | pdb_00009e2s

Apo TRiC in closed conformation

  • Classification: CHAPERONE
  • Organism(s): Homo sapiens
  • Expression System: Trichoplusia ni
  • Mutation(s): No 

  • Deposited: 2024-10-22 Released: 2025-10-08 
  • Deposition Author(s): Zhao, Y., Chiu, W.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Visualizing dynamic tubulin folding in chaperonin TRiC from nonnative nucleus to final native state.

Zhao, Y.Schmid, M.F.Chiu, W.

(2025) Nat Commun 16: 7878-7878

  • DOI: https://doi.org/10.1038/s41467-025-63016-x
  • Primary Citation of Related Structures:  
    9E2S

  • PubMed Abstract: 

    The folding nucleus (FN) initiates and enables an efficient protein folding pathway. Despite its essential role, the FN has long remained cryptic. Here we directly visualize the tubulin FN consisting of a nonnative, partially assembled Rossmann fold, in the closed chamber of human chaperonin TRiC. Chaperonin TRiC interacts with nonnatively folded secondary structure elements of tubulin, stabilizing the nucleus poised for transition into its first native domain tertiary structure. Through progressive folding into the native state, we observe that the unfolded sequence of tubulin undergoes drastic spatial rearrangement in the TRiC chamber to sample the conformational space, mediated by the highly dynamic CCT tails. The observed presence of individual nonnative secondary structure elements first in the nonnative FN and then around the incrementally folded native domains supports the hypothesis that tubulin folding in TRiC is a hierarchical process of nucleation, condensation and propagation in cooperation with TRiC subunits.


  • Organizational Affiliation
    • Department of Bioengineering, Stanford University, Stanford, CA, USA. yanyanz@stanford.edu.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit thetaA [auth B],
I [auth b]
547Homo sapiensMutation(s): 0 
Gene Names: CCT8C21orf112CCTQKIAA0002
EC: 3.6.1
UniProt & NIH Common Fund Data Resources
Find proteins for P50990 (Homo sapiens)
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PHAROS:  P50990
GTEx:  ENSG00000156261 
Entity Groups  
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UniProt GroupP50990
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit etaB [auth C],
J [auth c]
553Homo sapiensMutation(s): 0 
Gene Names: CCT7CCTHNIP7-1
EC: 3.6.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99832 (Homo sapiens)
Explore Q99832 
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PHAROS:  Q99832
GTEx:  ENSG00000135624 
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UniProt GroupQ99832
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit epsilonC [auth D],
K [auth d]
541Homo sapiensMutation(s): 0 
Gene Names: CCT5CCTEKIAA0098
EC: 3.6.1
UniProt & NIH Common Fund Data Resources
Find proteins for P48643 (Homo sapiens)
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PHAROS:  P48643
GTEx:  ENSG00000150753 
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UniProt GroupP48643
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit betaD [auth E],
L [auth e]
535Homo sapiensMutation(s): 0 
Gene Names: CCT299D8.1CCTB
EC: 3.6.1
UniProt & NIH Common Fund Data Resources
Find proteins for P78371 (Homo sapiens)
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GTEx:  ENSG00000166226 
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UniProt GroupP78371
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit deltaE [auth F],
M [auth f]
539Homo sapiensMutation(s): 0 
Gene Names: CCT4CCTDSRB
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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UniProt GroupP50991
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit alphaF [auth G],
N [auth g]
556Homo sapiensMutation(s): 0 
Gene Names: TCP1CCT1CCTA
EC: 3.6.1
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Find proteins for P17987 (Homo sapiens)
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PHAROS:  P17987
GTEx:  ENSG00000120438 
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UniProt GroupP17987
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit gammaG [auth H],
O [auth h]
545Homo sapiensMutation(s): 0 
Gene Names: CCT3CCTGTRIC5
EC: 3.6.1
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Find proteins for P49368 (Homo sapiens)
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GTEx:  ENSG00000163468 
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UniProt GroupP49368
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit zetaH [auth I],
P [auth i]
531Homo sapiensMutation(s): 0 
Gene Names: CCT6ACCT6CCTZ
EC: 3.6.1
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Find proteins for P40227 (Homo sapiens)
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GTEx:  ENSG00000146731 
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UniProt GroupP40227
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
AA [auth E]
BB [auth f]
DA [auth F]
DB [auth g]
HA [auth G]
AA [auth E],
BB [auth f],
DA [auth F],
DB [auth g],
HA [auth G],
IB [auth h],
JA [auth H],
LB [auth i],
MA [auth I],
PA [auth b],
R [auth B],
SA [auth c],
U [auth C],
UA [auth d],
XA [auth e],
Y [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 
AB [auth f]
EA [auth F]
EB [auth g]
FA [auth G]
HB [auth h]
AB [auth f],
EA [auth F],
EB [auth g],
FA [auth G],
HB [auth h],
JB [auth i],
KA [auth H],
LA [auth I],
OA [auth b],
S [auth B],
TA [auth c],
V [auth C],
W [auth D],
WA [auth d],
YA [auth e],
Z [auth E]
ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-UHFFFAOYSA-K
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
BA [auth E]
CA [auth F]
CB [auth f]
FB [auth g]
GA [auth G]
BA [auth E],
CA [auth F],
CB [auth f],
FB [auth g],
GA [auth G],
GB [auth h],
IA [auth H],
KB [auth i],
NA [auth I],
Q [auth B],
QA [auth b],
RA [auth c],
T [auth C],
VA [auth d],
X [auth D],
ZA [auth e]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207
RECONSTRUCTIONRELION4

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU24GM129541

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-08
    Type: Initial release