1JHN

Crystal Structure of the Lumenal Domain of Calnexin

• PDB DOI: https://doi.org/10.2210/pdb1JHN/pdb

• Classification: CHAPERONE
• Organism(s): Canis lupus familiaris
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2001-06-28 Released: 2001-10-10 
• Deposition Author(s): Schrag, J.D., Bergeron, J.M., Li, Y., Borisova, S., Hahn, M., Thomas, D.Y., Cygler, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.377 (Depositor), 0.400 (DCC) 
• R-Value Work: 
  0.327 (Depositor), 0.342 (DCC) 

Literature

The Structure of calnexin, an ER chaperone involved in quality control of protein folding.

Schrag, J.D., Bergeron, J.J., Li, Y., Borisova, S., Hahn, M., Thomas, D.Y., Cygler, M.

(2001) Mol Cell 8: 633-644

• PubMed: 11583625 
• DOI: https://doi.org/10.1016/s1097-2765(01)00318-5
• Primary Citation of Related Structures:  
  1JHN


• PubMed Abstract: 
  

  The three-dimensional structure of the lumenal domain of the lectin-like chaperone calnexin determined to 2.9 A resolution reveals an extended 140 A arm inserted into a beta sandwich structure characteristic of legume lectins. The arm is composed of tandem repeats of two proline-rich sequence motifs which interact with one another in a head-to-tail fashion. Identification of the ligand binding site establishes calnexin as a monovalent lectin, providing insight into the mechanism by which the calnexin family of chaperones interacts with monoglucosylated glycoproteins.

---

Organizational Affiliation: 

Biotechnology Research Institute, NRC, 6100 Royalmount Avenue, Montreal, Quebec H4P 2R2, Canada. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 48.33 kDa 
• Atom Count: 2,854 
• Modelled Residue Count: 380 
• Deposited Residue Count: 424 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
calnexin	A	424	Canis lupus familiaris	Mutation(s): 0
UniProt
Find proteins for P24643 (Canis lupus familiaris) Explore P24643  Go to UniProtKB:  P24643

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.377 (Depositor), 0.400 (DCC) 
• R-Value Work:  0.327 (Depositor), 0.342 (DCC) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.772	α = 90
b = 85.772	β = 90
c = 143.476	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-10-10 
Deposition Author(s): Schrag, J.D., Bergeron, J.M., Li, Y., Borisova, S., Hahn, M., Thomas, D.Y., Cygler, M.

Revision History  

• Version 1.0: 2001-10-10
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary