Crystal structure of Bovine 3 Glu-Osteocalcin.

Experimental Data Snapshot

  • Resolution: 1.88 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


X-ray crystal structure of bovine 3 Glu-osteocalcin.

Malashkevich, V.N.Almo, S.C.Dowd, T.L.

(2013) Biochemistry 52: 8387-8392

  • DOI: https://doi.org/10.1021/bi4010254
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The 3 Glu form of osteocalcin (3 Glu-OCN) is increased in serum during low vitamin K intake or oral anticoagulant use (warfarin). Previous reports using circular dichroism show it is less structured than 3 Gla Ca²⁺-osteocalcin and does not bind strongly to bone mineral. Recent studies have suggested a role for 3 Glu-OCN as a potential regulator of glucose metabolism. A G-protein-coupled receptor, GPRC6a, found in the pancreas and testes was identified as the putative osteocalcin receptor. The purpose of this study is to determine the high-resolution structure of bovine 3 Glu-OCN, using X-ray crystallography, to understand molecular interactions with mineral and the GPRC6a receptor. Diffraction quality crystals of thermally decarboxylated bovine osteocalcin were grown, and the crystal structure was determined to 1.88 Å resolution. The final refined structure contained residues 17-47 and, like 3 Gla Ca²⁺-OCN, consisted of three α-helices surrounding a hydrophobic core, a C23-C29 disulfide bond between two of the helices, and no bound Ca²⁺. Thus, the helical structure of 3 Glu-OCN is Ca²⁺-independent but similar to that of 3 Gla Ca²⁺-OCN. A reduced level of mineral binding could result from a lower number of Ca²⁺ coordinating ligands on 3 Glu-OCN. The structure suggests the GPRC6a receptor may respond to helical osteocalcin and will aid in providing molecular mechanistic insight into the role of 3 Glu-OCN in glucose homeostasis.

  • Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine , Bronx, New York 10461, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
33Bos taurusMutation(s): 0 
Membrane Entity: Yes 
Find proteins for P02820 (Bos taurus)
Explore P02820 
Go to UniProtKB:  P02820
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02820
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.88 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.761α = 90
b = 42.761β = 90
c = 37.987γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-3000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-27
    Type: Initial release
  • Version 1.1: 2014-05-07
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Refinement description