Crystal structure of porcine osteocalcin

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 

wwPDB Validation   3D Report Full Report

This is version 2.0 of the entry. See complete history


Bone recognition mechanism of porcine osteocalcin from crystal structure.

Hoang, Q.Q.Sicheri, F.Howard, A.J.Yang, D.S.

(2003) Nature 425: 977-980

  • DOI: https://doi.org/10.1038/nature02079
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Osteocalcin is the most abundant noncollagenous protein in bone, and its concentration in serum is closely linked to bone metabolism and serves as a biological marker for the clinical assessment of bone disease. Although its precise mechanism of action is unclear, osteocalcin influences bone mineralization, in part through its ability to bind with high affinity to the mineral component of bone, hydroxyapatite. In addition to binding to hydroxyapatite, osteocalcin functions in cell signalling and the recruitment of osteoclasts and osteoblasts, which have active roles in bone resorption and deposition, respectively. Here we present the X-ray crystal structure of porcine osteocalcin at 2.0 A resolution, which reveals a negatively charged protein surface that coordinates five calcium ions in a spatial orientation that is complementary to calcium ions in a hydroxyapatite crystal lattice. On the basis of our findings, we propose a model of osteocalcin binding to hydroxyapatite and draw parallels with other proteins that engage crystal lattices.

  • Organizational Affiliation

    Department of Biochemistry, Faculty of Health Science, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Osteocalcin49Sus scrofaMutation(s): 0 
Find proteins for Q8HYY9 (Sus scrofa)
Explore Q8HYY9 
Go to UniProtKB:  Q8HYY9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8HYY9
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.491α = 90
b = 51.491β = 90
c = 35.389γ = 120
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-11-11
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 2.0: 2019-02-06
    Changes: Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary