The crystal structure of Hsp40 Ydj1

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.269 
  • R-Value Observed: 0.269 

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The crystal structure of the yeast Hsp40 Ydj1 complexed with its peptide substrate.

Li, J.Qian, X.Sha, B.

(2003) Structure 11: 1475-1483

  • DOI: https://doi.org/10.1016/j.str.2003.10.012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The mechanisms by which Hsp40 functions as a molecular chaperone to recognize and bind non-native polypeptides is not understood. We have identified a peptide substrate for Ydj1, a member of the type I Hsp40 from yeast. The structure of the Ydj1 peptide binding fragment and its peptide substrate complex was determined to 2.7 A resolution. The complex structure reveals that Ydj1 peptide binding fragment forms an L-shaped molecule constituted by three domains. The domain I exhibits a similar protein folds as domain III while the domain II contains two Zinc finger motifs. The peptide substrate binds Ydj1 by forming an extra beta strand with domain I of Ydj1. The Leucine residue in the middle of the peptide substrate GWLYEIS inserts its side chain into a hydrophobic pocket formed on the molecular surface of Ydj1 domain I. The Zinc finger motifs located in the Ydj1 domain II are not in the vicinity of peptide substrate binding site.

  • Organizational Affiliation

    Department of Cell Biology, Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial protein import protein MAS5248Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: MAS5 OR YDJ1 OR YNL064C OR N2418 OR YNL2418C
Find proteins for P25491 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25491 
Go to UniProtKB:  P25491
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25491
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Seven residue peptide7N/AMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.269 
  • R-Value Observed: 0.269 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.025α = 90
b = 55.025β = 90
c = 161.87γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2004-01-13 
  • Deposition Author(s): Li, J., Sha, B.

Revision History  (Full details and data files)

  • Version 1.0: 2004-01-13
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations