5NB8

Structure of vWC domain from CCN3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural analyses of von Willebrand factor C domains of collagen 2A and CCN3 reveal an alternative mode of binding to bone morphogenetic protein-2.

Xu, E.R.Blythe, E.E.Fischer, G.Hyvonen, M.

(2017) J. Biol. Chem. 292: 12516-12527

  • DOI: 10.1074/jbc.M117.788992
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bone morphogenetic proteins (BMPs) are secreted growth factors that promote differentiation processes in embryogenesis and tissue development. Regulation of BMP signaling involves binding to a variety of extracellular proteins, among which are many v ...

    Bone morphogenetic proteins (BMPs) are secreted growth factors that promote differentiation processes in embryogenesis and tissue development. Regulation of BMP signaling involves binding to a variety of extracellular proteins, among which are many von Willebrand factor C (vWC) domain-containing proteins. Although the crystal structure of the complex of crossveinless-2 (CV-2) vWC1 and BMP-2 previously revealed one mode of the vWC/BMP-binding mechanism, other vWC domains may bind to BMP differently. Here, using X-ray crystallography, we present for the first time structures of the vWC domains of two proteins thought to interact with BMP-2: collagen IIA and matricellular protein CCN3. We found that these two vWC domains share a similar N-terminal fold that differs greatly from that in CV-2 vWC, which comprises its BMP-2-binding site. We analyzed the ability of these vWC domains to directly bind to BMP-2 and detected an interaction only between the collagen IIa vWC and BMP-2. Guided by the collagen IIa vWC domain crystal structure and conservation of surface residues among orthologous domains, we mapped the BMP-binding epitope on the subdomain 1 of the vWC domain. This binding site is different from that previously observed in the complex between CV-2 vWC and BMP-2, revealing an alternative mode of interaction between vWC domains and BMPs.


    Organizational Affiliation

    From the Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein NOV homolog
A, B, C, D
97Rattus norvegicusMutation(s): 0 
Gene Names: Ccn3 (Nov)
Find proteins for Q9QZQ5 (Rattus norvegicus)
Go to UniProtKB:  Q9QZQ5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

Download SDF File 
Download CCD File 
A, B, C, D
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.189 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 38.400α = 75.30
b = 43.100β = 82.00
c = 72.300γ = 89.90
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
PHENIXrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-03-01 
  • Released Date: 2017-06-14 
  • Deposition Author(s): Xu, E.-R., Hyvonen, M.

Revision History 

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-08-09
    Type: Database references