1ZLM

Crystal structure of the SH3 domain of human osteoclast stimulating factor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the SH3 domain of human osteoclast-stimulating factor at atomic resolution.

Chen, L.Wang, Y.Wells, D.Toh, D.Harold, H.Zhou, J.DiGiammarino, E.Meehan, E.J.

(2006) Acta Crystallogr.,Sect.F 62: 844-848

  • DOI: 10.1107/S1744309106030004

  • PubMed Abstract: 
  • Osteoclast-stimulating factor (OSF) is an intracellular signaling protein, produced by osteoclasts themselves, that enhances osteoclast formation and bone resorption. It is thought to act via an Src-related signaling pathway and contains SH3 and anky ...

    Osteoclast-stimulating factor (OSF) is an intracellular signaling protein, produced by osteoclasts themselves, that enhances osteoclast formation and bone resorption. It is thought to act via an Src-related signaling pathway and contains SH3 and ankyrin-repeat domains which are involved in protein-protein interactions. As part of a structure-based anti-bone-loss drug-design program, the atomic resolution X-ray structure of the recombinant human OSF SH3 domain (hOSF-SH3) has been determined. The domain, residues 12-72, yielded crystals that diffracted to the ultrahigh resolution of 1.07 A. The overall structure shows a characteristic SH3 fold consisting of two perpendicular beta-sheets that form a beta-barrel. Structure-based sequence alignment reveals that the putative proline-rich peptide-binding site of hOSF-SH3 consists of (i) residues that are highly conserved in the SH3-domain family, including residues Tyr21, Phe23, Trp49, Pro62, Asn64 and Tyr65, and (ii) residues that are less conserved and/or even specific to hOSF, including Thr22, Arg26, Thr27, Glu30, Asp46, Thr47, Asn48 and Leu60, which might be key to designing specific inhibitors for hOSF to fight osteoporosis and related bone-loss diseases. There are a total of 13 well defined water molecules forming hydrogen bonds with the above residues in and around the peptide-binding pocket. Some of those water molecules might be important for drug-design approaches. The hOSF-SH3 structure at atomic resolution provides an accurate framework for structure-based design of its inhibitors.


    Organizational Affiliation

    Laboratory for Structural Biology, University of Alabama in Huntsville, Huntsville, Alabama 35899, USA. chenlq@uah.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Osteoclast stimulating factor 1
A
58Homo sapiensMutation(s): 0 
Gene Names: OSTF1
Find proteins for Q92882 (Homo sapiens)
Go to Gene View: OSTF1
Go to UniProtKB:  Q92882
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.158 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 36.810α = 90.00
b = 80.480β = 90.00
c = 49.160γ = 90.00
Software Package:
Software NamePurpose
SHELXmodel building
HKL-2000data reduction
SCALEPACKdata scaling
SHELXL-97refinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-05-16
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance