Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 82.77 kDa 
• Atom Count: 5878 
• Residue Count: 718 
• Unique protein chains: 1

3IEG

Crystal Structure of P58(IPK) TPR Domain at 2.5 A

• DOI: 10.2210/pdb3IEG/pdb

• Classification: CHAPERONE
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-22 Released: 2010-03-31 
• Deposition Author(s): Tao, J., Sha, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 0.284 
• R-Value Work: 0.245 
• R-Value Observed: 0.247 

Literature

Crystal Structure of P58(IPK) TPR Fragment Reveals the Mechanism for its Molecular Chaperone Activity in UPR.

Tao, J., Petrova, K., Ron, D., Sha, B.

(2010) J Mol Biol 64: 108-110

• PubMed: 20184891 
• DOI: 10.1016/j.jmb.2010.02.028
• Structures With Same Primary Citation


• PubMed Abstract: 
  

P58(IPK) might function as an endoplasmic reticulum molecular chaperone to maintain protein folding homeostasis during unfolded protein responses. P58(IPK) contains nine tetratricopeptide repeat (TPR) motifs and a C-terminal J-domain within its primary sequence. To investigate the mechanism by which P58(IPK) functions to promote protein folding within the endoplasmic reticulum, we have determined the crystal structure of P58(IPK) TPR fragment to 2.5 A resolution by the SAD method. The crystal structure of P58(IPK) revealed three domains (I-III) with similar folds and each domain contains three TPR motifs. An ELISA assay indicated that P58(IPK) acts as a molecular chaperone by interacting with misfolded proteins such as luciferase and rhodanese. The P58(IPK) structure reveals a conserved hydrophobic patch located in domain I that might be involved in binding the misfolded polypeptides. Structure-based mutagenesis for the conserved hydrophobic residues located in domain I significantly reduced the molecular chaperone activity of P58(IPK).

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Organizational Affiliation: 

Department of Cell Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DnaJ homolog subfamily C member 3	A, B	359	Mus musculus	Mutation(s): 0  Gene Names: Dnajc3, P58(IPK), P58ipk
Find proteins for Q91YW3 (Mus musculus) Go to UniProtKB:  Q91YW3

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A,B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 0.284 
• R-Value Work: 0.245 
• R-Value Observed: 0.247 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.041	α = 90
b = 93.186	β = 119.5
c = 84.412	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SOLVE	phasing
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-07-22 
• Released Date: 2010-03-31 
Deposition Author(s): Tao, J., Sha, B.

Revision History 

• Version 1.0: 2010-03-31
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description