4FD2

Crystal structure of the C-terminal domain of ClpB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.279 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural basis for intersubunit signaling in a protein disaggregating machine.

Biter, A.B.Lee, S.Sung, N.Tsai, F.T.

(2012) Proc Natl Acad Sci U S A 109: 12515-12520

  • DOI: https://doi.org/10.1073/pnas.1207040109
  • Primary Citation of Related Structures:  
    4FCT, 4FCV, 4FCW, 4FD2

  • PubMed Abstract: 

    ClpB is a ring-forming, ATP-dependent protein disaggregase that cooperates with the cognate Hsp70 system to recover functional protein from aggregates. How ClpB harnesses the energy of ATP binding and hydrolysis to facilitate the mechanical unfolding of previously aggregated, stress-damaged proteins remains unclear. Here, we present crystal structures of the ClpB D2 domain in the nucleotide-bound and -free states, and the fitted cryoEM structure of the D2 hexamer ring, which provide a structural understanding of the ATP power stroke that drives protein translocation through the ClpB hexamer. We demonstrate that the conformation of the substrate-translocating pore loop is coupled to the nucleotide state of the cis subunit, which is transmitted to the neighboring subunit via a conserved but structurally distinct intersubunit-signaling pathway common to diverse AAA+ machines. Furthermore, we found that an engineered, disulfide cross-linked ClpB hexamer is fully functional biochemically, suggesting that ClpB deoligomerization is not required for protein disaggregation.


  • Organizational Affiliation

    Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chaperone protein ClpBA,
B,
C [auth D]
308Thermus thermophilus HB8Mutation(s): 1 
Gene Names: clpBTTHA1487
UniProt
Find proteins for Q9RA63 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q9RA63 
Go to UniProtKB:  Q9RA63
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RA63
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.279 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.775α = 90
b = 129.775β = 90
c = 129.401γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-18
    Type: Initial release
  • Version 1.1: 2012-08-22
    Changes: Database references
  • Version 1.2: 2018-04-18
    Changes: Data collection
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations