Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 28386.40 
• Atom Count: 1815 
• Residue Count: 255 
• Unique protein chains: 2

1NLT

The crystal structure of Hsp40 Ydj1

• DOI: 10.2210/pdb1NLT/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 1 


• 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: 2.7 Å
• R-Value Free: 0.296 
• R-Value Work: 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 


• 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

Find similar proteins by: Sequence  |  Structure

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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Seven residue peptide	B	7	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.296 
• R-Value Work: 0.269 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 55.025	α = 90.00
b = 55.025	β = 90.00
c = 161.870	γ = 120.00

Software Package:

Software Name	Purpose
SOLVE	phasing
SCALEPACK	data scaling
DENZO	data reduction
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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance