3BK3 | pdb_00003bk3

Crystal structure of the complex of BMP-2 and the first Von Willebrand domain type C of Crossveinless-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.245 (Depositor), 0.251 (DCC) 
  • R-Value Work: 
    0.203 (Depositor) 
  • R-Value Observed: 
    0.205 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3BK3

This is version 1.3 of the entry. See complete history

Literature

Crystal structure analysis reveals how the Chordin family member crossveinless 2 blocks BMP-2 receptor binding

Zhang, J.-L.Qiu, L.-Y.Kotzsch, A.Weidauer, S.Patterson, L.Hammerschmidt, M.Sebald, W.Mueller, T.D.

(2008) Dev Cell 14: 739-750

  • DOI: https://doi.org/10.1016/j.devcel.2008.02.017
  • Primary Citation Related Structures: 
    3BK3

  • PubMed Abstract: 

    Crossveinless 2 (CV-2) is an extracellular BMP modulator protein belonging to the Chordin family. During development it is expressed at sites of high BMP signaling and like Chordin CV-2 can either enhance or inhibit BMP activity. CV-2 binds to BMP-2 via its N-terminal Von Willebrand factor type C (VWC) domain 1. Here we report the structure of the complex between CV-2 VWC1 and BMP-2. The tripartite VWC1 binds BMP-2 only through a short N-terminal segment, called clip, and subdomain (SD) 1. Mutational analysis establishes that the clip segment and SD1 together create high-affinity BMP-2 binding. All four receptor-binding sites of BMP-2 are blocked in the complex, demonstrating that VWC1 acts as competitive inhibitor for all receptor types. In vivo experiments reveal that the BMP-enhancing (pro-BMP) activity of CV-2 is independent of BMP-2 binding by VWC1, showing that pro- and anti-BMP activities are structurally separated in CV-2.


  • Organizational Affiliation
    • Department of Physiological Chemistry II, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 40.14 kDa 
  • Atom Count: 2,635 
  • Modeled Residue Count: 342 
  • Deposited Residue Count: 362 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bone morphogenetic protein 2
A, B
114Homo sapiensMutation(s): 2 
Gene Names: BMP2BMP2A
UniProt & NIH Common Fund Data Resources
Find proteins for P12643 (Homo sapiens)
Explore P12643 
Go to UniProtKB:  P12643
PHAROS:  P12643
GTEx:  ENSG00000125845 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12643
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Crossveinless 2
C, D
67Danio rerioMutation(s): 0 
Gene Names: crossveinless-2
UniProt
Find proteins for Q5D734 (Danio rerio)
Explore Q5D734 
Go to UniProtKB:  Q5D734
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5D734
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.245 (Depositor), 0.251 (DCC) 
  • R-Value Work:  0.203 (Depositor) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.75α = 90
b = 83.75β = 90
c = 139.85γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
SHARPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-05-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references
  • Version 1.3: 2024-10-16
    Changes: Data collection, Structure summary