4JU5

Crystal structure of the dimeric form of the bb' domains of human protein disulfide isomerase

• PDB DOI: https://doi.org/10.2210/pdb4JU5/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2013-03-24 Released: 2014-02-19 
• Deposition Author(s): Bastos-Aristizabal, S., Kozlov, G., Gehring, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.290 
• R-Value Work: 0.243 
• R-Value Observed: 0.245 

Starting Models: experimental

Literature

Structural insight into the dimerization of human protein disulfide isomerase.

Bastos-Aristizabal, S., Kozlov, G., Gehring, K.

(2014) Protein Sci 23: 618-626

• PubMed: 24549644 
• DOI: https://doi.org/10.1002/pro.2444
• Primary Citation of Related Structures:  
  4JU5


• PubMed Abstract: 
  

  Protein disulfide isomerases (PDIs) are responsible for catalyzing the proper oxidation and isomerization of disulfide bonds of newly synthesized proteins in the endoplasmic reticulum (ER). Here, it is shown that human PDI (PDIA1) dimerizes in vivo and proposed that the dimerization of PDI has physiological relevance by autoregulating its activity. The crystal structure of the dimeric form of noncatalytic bb' domains of human PDIA1 determined to 2.3 Å resolution revealed that the formation of dimers occludes the substrate binding site and may function as a mechanism to regulate PDI activity in the ER.

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Organizational Affiliation: 

Department of Biochemistry, Groupe de recherche axé sur la structure des protéines, McGill University, 3649 Promenade Sir William Osler, Montréal, Québec, H3G 0B1, Canada.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 53.67 kDa 
• Atom Count: 3,101 
• Modelled Residue Count: 397 
• Deposited Residue Count: 476 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein disulfide-isomerase	A, B	238	Homo sapiens	Mutation(s): 0  Gene Names: P4HB, ERBA2L, PDI, PDIA1, PO4DB EC: 5.3.4.1
UniProt & NIH Common Fund Data Resources
Find proteins for P07237 (Homo sapiens) Explore P07237  Go to UniProtKB:  P07237
PHAROS:  P07237 GTEx:  ENSG00000185624

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.290 
• R-Value Work: 0.243 
• R-Value Observed: 0.245 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.521	α = 81.85
b = 45.718	β = 92.15
c = 55.149	γ = 80.02

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-19 
Deposition Author(s): Bastos-Aristizabal, S., Kozlov, G., Gehring, K.

Revision History  

• Version 1.0: 2014-02-19
  Type: Initial release
  
• Version 1.1: 2014-03-05
  Changes: Database references
• Version 1.2: 2014-03-19
  Changes: Database references
• Version 1.3: 2014-05-07
  Changes: Database references
• Version 1.4: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.5: 2023-09-20
  Changes: Data collection, Database references, Refinement description