8I6J

The focused refinement of CCT3-PhLP2A from TRiC-PhLP2A complex in the open state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.82 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A structural vista of phosducin-like PhLP2A-chaperonin TRiC cooperation during the ATP-driven folding cycle.

Park, J.Kim, H.Gestaut, D.Lim, S.Opoku-Nsiah, K.A.Leitner, A.Frydman, J.Roh, S.H.

(2024) Nat Commun 15: 1007-1007

  • DOI: https://doi.org/10.1038/s41467-024-45242-x
  • Primary Citation of Related Structures:  
    8I1U, 8I6J, 8I9Q, 8I9U, 8IB8

  • PubMed Abstract: 

    Proper cellular proteostasis, essential for viability, requires a network of chaperones and cochaperones. ATP-dependent chaperonin TRiC/CCT partners with cochaperones prefoldin (PFD) and phosducin-like proteins (PhLPs) to facilitate folding of essential eukaryotic proteins. Using cryoEM and biochemical analyses, we determine the ATP-driven cycle of TRiC-PFD-PhLP2A interaction. PhLP2A binds to open apo-TRiC through polyvalent domain-specific contacts with its chamber's equatorial and apical regions. PhLP2A N-terminal H3-domain binding to subunits CCT3/4 apical domains displace PFD from TRiC. ATP-induced TRiC closure rearranges the contacts of PhLP2A domains within the closed chamber. In the presence of substrate, actin and PhLP2A segregate into opposing chambers, each binding to positively charged inner surface residues from CCT1/3/6/8. Notably, actin induces a conformational change in PhLP2A, causing its N-terminal helices to extend across the inter-ring interface to directly contact a hydrophobic groove in actin. Our findings reveal an ATP-driven PhLP2A structural rearrangement cycle within the TRiC chamber to facilitate folding.


  • Organizational Affiliation

    School of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosducin-like protein 3A [auth Q]239Homo sapiensMutation(s): 0 
Gene Names: PDCL3PhLP2A
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H2J4 (Homo sapiens)
Explore Q9H2J4 
Go to UniProtKB:  Q9H2J4
GTEx:  ENSG00000115539 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H2J4
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit gammaB [auth C]545Homo sapiensMutation(s): 0 
Gene Names: CCT3CCTGTRIC5
UniProt & NIH Common Fund Data Resources
Find proteins for P49368 (Homo sapiens)
Explore P49368 
Go to UniProtKB:  P49368
PHAROS:  P49368
GTEx:  ENSG00000163468 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49368
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
C
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.82 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19
MODEL REFINEMENTCoot0.9.6
RECONSTRUCTIONcryoSPARC3.2.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-31
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Database references