Crystal structure of human Hsp40 Hdj1 peptide-binding domain

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.229 

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Peptide-binding sites as revealed by the crystal structures of the human Hsp40 Hdj1 C-terminal domain in complex with the octapeptide from human Hsp70

Suzuki, H.Noguchi, S.Arakawa, H.Tokida, T.Hashimoto, M.Satow, Y.

(2010) Biochemistry 49: 8577-8584

  • DOI: https://doi.org/10.1021/bi100876n
  • Primary Citation of Related Structures:  
    3AGX, 3AGY, 3AGZ

  • PubMed Abstract: 

    Heat shock protein (Hsp) 40s play essential roles in cellular processes by cooperating with Hsp70 proteins. Hsp40 proteins recognize non-native polypeptides, deliver these peptides to Hsp70 proteins, and stimulate the ATPase activity of Hsp70 proteins to facilitate the correct folding of the polypeptides. We have determined the crystal structures of the C-terminal peptide-binding domain of human Hsp40 Hdj1 (CTD) and of its complex with the C-terminal octapeptide of human Hsp70, (634')GPTIEEVD(641'). CTD exists as a twisted, horseshoe-shaped homodimer. The protomer consists of two domains, I and II, with similar topologies. The octapeptides are located in two sites, 1 and 2, of domain I. In site 1, the octapeptide forms an antiparallel β-sheet with CTD. The negatively charged residues of the EEVD motif in the octapeptide form electrostatic interactions with the positively charged Lys residues of CTD. The Ile side chain of the octapeptide fits into the narrow concave formed by the hydrophobic residues of CTD. In site 2, the octapeptide also forms an antiparallel β-sheet with CTD, and the EEVD motif forms electrostatic interactions. The side chains of Pro and Ile of the octapeptide interact with the hydrophobic surface region of CTD site 2, which is broader and shallower than the concave binding region of site 1. This region seems to be capable of binding hydrophobic side chains that are bulkier than the Ile side chain. The roles of these two peptide-binding sites of Hdj1 are discussed.

  • Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DnaJ homolog subfamily B member 1
A, B
181Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P25685 (Homo sapiens)
Explore P25685 
Go to UniProtKB:  P25685
GTEx:  ENSG00000132002 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25685
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.85 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.252α = 90
b = 40.921β = 96.62
c = 62.65γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references