Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 28.39 kDa 
• Atom Count: 1962 
• Modelled Residue Count: 235 
• Deposited Residue Count: 255 
• Unique protein chains: 2

1NLT

The crystal structure of Hsp40 Ydj1

• PDB DOI: 10.2210/pdb1NLT/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2003-01-07 Released: 2004-01-13 
• Deposition Author(s): Li, J., Sha, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.296 
• R-Value Work: 0.269 
• R-Value Observed: 0.269 

Literature

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

Li, J., Qian, X., Sha, B.

(2003) Structure 11: 1475-1483

• PubMed: 14656432 
• DOI: 10.1016/j.str.2003.10.012
• Primary Citation of Related Structures:  
  1NLT


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial protein import protein MAS5	A	248	Saccharomyces cerevisiae	Mutation(s): 1  Gene Names: MAS5 OR YDJ1 OR YNL064C OR N2418 OR YNL2418C
UniProt
Find proteins for P25491 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25491  Go to UniProtKB:  P25491

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Seven residue peptide	B	7	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 55.025	α = 90
b = 55.025	β = 90
c = 161.87	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-01-07 
• Released Date: 2004-01-13 
Deposition Author(s): Li, J., Sha, B.

Revision History  

• 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