3POW | pdb_00003pow

Crystal structure of the globular domain of human calreticulin

• PDB DOI: https://doi.org/10.2210/pdb3POW/pdb

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


• Deposited: 2010-11-23 Released: 2011-03-09 
• Deposition Author(s): Gaboriaud, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.191 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

X-ray structure of the human calreticulin globular domain reveals a Peptide-binding area and suggests a multi-molecular mechanism

Chouquet, A., Paidassi, H., Ling, W.L., Frachet, P., Houen, G., Arlaud, G.J., Gaboriaud, C.

(2011) PLoS One 6: e17886-e17886

• PubMed: 21423620 
• DOI: https://doi.org/10.1371/journal.pone.0017886
• Primary Citation of Related Structures:  
  3POS, 3POW


• PubMed Abstract: 
  

  In the endoplasmic reticulum, calreticulin acts as a chaperone and a Ca(2+)-signalling protein. At the cell surface, it mediates numerous important biological effects. The crystal structure of the human calreticulin globular domain was solved at 1.55 Å resolution. Interactions of the flexible N-terminal extension with the edge of the lectin site are consistently observed, revealing a hitherto unidentified peptide-binding site. A calreticulin molecular zipper, observed in all crystal lattices, could further extend this site by creating a binding cavity lined by hydrophobic residues. These data thus provide a first structural insight into the lectin-independent binding properties of calreticulin and suggest new working hypotheses, including that of a multi-molecular mechanism.

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Organizational Affiliation: 

Institut de Biologie Structurale Jean-Pierre Ebel, CEA, Grenoble, France.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 30.19 kDa 
• Atom Count: 2,370 
• Modeled Residue Count: 251 
• Deposited Residue Count: 265 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
calreticulin	A	265	Homo sapiens	Mutation(s): 0  Gene Names: CALR, CRTC
UniProt & NIH Common Fund Data Resources
Find proteins for P27797 (Homo sapiens) Explore P27797  Go to UniProtKB:  P27797
PHAROS:  P27797 GTEx:  ENSG00000179218

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: 1.55 Å
• R-Value Free:  0.191 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.89	α = 90
b = 70.39	β = 90
c = 91.82	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction
PHASER	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-09 
Deposition Author(s): Gaboriaud, C.

Revision History  

• Version 1.0: 2011-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-08-09
  Changes: Data collection, Refinement description, Source and taxonomy
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary