3AGY

Crystal structure of human Hsp40 Hdj1 peptide-binding domain complexed with a C-terminal peptide of Hsp70


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1021/bi100876n
  • Primary Citation of Related Structures:  

  • 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 protein ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DnaJ homolog subfamily B member 1
A, B
181Homo sapiensMutation(s): 0 
Gene Names: DNAJB1 (DNAJ1, HDJ1, HSPF1)
Find proteins for P25685 (Homo sapiens)
Go to Gene View: DNAJB1
Go to UniProtKB:  P25685
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
peptide of Heat shock cognate 71 kDa protein
C, D, F
8Homo sapiensMutation(s): 0 
Gene Names: HSPA8 (HSC70, HSP73, HSPA10)
Find proteins for P11142 (Homo sapiens)
Go to Gene View: HSPA8
Go to UniProtKB:  P11142
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.225 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 104.746α = 90.00
b = 41.132β = 97.42
c = 62.865γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction
REFMACrefinement
HKL-2000data collection
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance