1Q8H

Crystal structure of porcine osteocalcin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.255 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

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: 10.1038/nature02079

  • 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 acti ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Osteocalcin
A
49Sus scrofaMutation(s): 0 
Gene Names: BGLAP
Find proteins for Q8HYY9 (Sus scrofa)
Go to Gene View: BGLAP
Go to UniProtKB:  Q8HYY9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CGU
Query on CGU
A
L-PEPTIDE LINKINGC6 H9 N O6GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.255 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 51.491α = 90.00
b = 51.491β = 90.00
c = 35.389γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MAR345data collection
SOLVEphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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