3BMP

HUMAN BONE MORPHOGENETIC PROTEIN-2 (BMP-2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of human bone morphogenetic protein-2 at 2.7 A resolution.

Scheufler, C.Sebald, W.Hulsmeyer, M.

(1999) J Mol Biol 287: 103-115

  • DOI: 10.1006/jmbi.1999.2590
  • Primary Citation of Related Structures:  
    3BMP

  • PubMed Abstract: 
  • Homodimeric bone morphogenetic protein-2 (BMP-2) is a member of the transforming growth factor beta (TGF-beta) superfamily that induces bone formation and regeneration, and determines important steps during early stages of embryonic development in ve ...

    Homodimeric bone morphogenetic protein-2 (BMP-2) is a member of the transforming growth factor beta (TGF-beta) superfamily that induces bone formation and regeneration, and determines important steps during early stages of embryonic development in vertebrates and non-vertebrates. BMP-2 can interact with two types of receptor chains, as well as with proteins of the extracellular matrix and several regulatory proteins. We report here the crystal structure of human BMP-2 determined by molecular replacement and refined to an R-value of 24.2 % at 2.7 A resolution. A common scaffold of BMP-2, BMP-7 and the TGF-betas, i.e. the cystine-knot motif and two finger-like double-stranded beta-sheets, can be superimposed with r. m.s. deviations of around 1 A. In contrast to the TGF-betas, the structure of BMP-2 shows differences in the flexibility of the N terminus and the orientation of the central alpha-helix as well as two external loops at the fingertips with respect to the scaffold. This is also known from the BMP-7 model. Small secondary structure elements in the loop regions of BMP-2 and BMP-7 seem to be specific for the respective BMP-subgroup. Two identical helix-finger clefts and two distinct cavities located around the central 2-fold axis of the dimer show characteristic shapes, polarity and surface charges. The possible function of these specific features in the interaction of BMP-2 with its binding partners is discussed.


    Related Citations: 
    • Human Bone Morphogenetic Protein 2 Contains a Heparin-Binding Site which Modifies its Biological Activity
      Ruppert, R., Hoffmann, E., Sebald, W.
      (1996) Eur J Biochem 237: 295

    Organizational Affiliation

    Physiological Chemistry II, University of Würzburg, Würzburg, 97074, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (BONE MORPHOGENETIC PROTEIN 2 (BMP-2))A114Homo sapiensMutation(s): 0 
Gene Names: BMP2BMP2A
Find proteins for P12643 (Homo sapiens)
Explore P12643 
Go to UniProtKB:  P12643
NIH Common Fund Data Resources
PHAROS  P12643
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.242 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.44α = 90
b = 91.44β = 90
c = 107.75γ = 120
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-03-12
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2018-04-04
    Changes: Data collection