2GOO

Ternary Complex of BMP-2 bound to BMPR-Ia-ECD and ActRII-ECD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the ternary signaling complex of a TGF-beta superfamily member.

Allendorph, G.P.Vale, W.W.Choe, S.

(2006) Proc.Natl.Acad.Sci.Usa 103: 7643-7648

  • DOI: 10.1073/pnas.0602558103

  • PubMed Abstract: 
  • The crystal structure of the complete signaling complex formed between bone morphogenetic protein 2 (BMP-2) and the extracellular domains (ECDs) of its type I receptor [bone morphogenetic protein receptor type Ia (BMPR-Ia)-ECD] and its type II recept ...

    The crystal structure of the complete signaling complex formed between bone morphogenetic protein 2 (BMP-2) and the extracellular domains (ECDs) of its type I receptor [bone morphogenetic protein receptor type Ia (BMPR-Ia)-ECD] and its type II receptor [activin receptor type II (ActRII)-ECD] shows two fundamental structural constraints for receptor assembly. First, the homodimeric BMP-2 ligand assembles two pairs of each receptor symmetrically, where each of the receptor ECDs does not make physical contact. Therefore, conformational communication between receptor ECDs, if any, should be propagated through the central ligand. Second, the type I and II receptor interfaces of the complex, when compared with those of binary complexes such as BMP-2/BMPR Ia-ECD, BMP-7/ActRII-ECD, and activin/ActRIIb-ECD, respectively, show there are common sets of positions repeatedly used by both ligands and receptors. Therefore, specificity-determining amino acid differences at the receptor interfaces should also account for the disparity in affinity of individual receptors for different ligand subunits. We find that a specific mutation to BMP-2 increases its affinity to ActRII-ECD by 5-fold. These results together establish that the specific signaling output is largely determined by two variables, the ligand-receptor pair identity and the mode of cooperative assembly of relevant receptors governed by the ligand flexibility in a membrane-restricted manner.


    Organizational Affiliation

    Structural Biology Laboratory, The Salk Institute, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bone morphogenetic protein 2
A, D
114Homo sapiensMutation(s): 0 
Gene Names: BMP2 (BMP2A)
Find proteins for P12643 (Homo sapiens)
Go to Gene View: BMP2
Go to UniProtKB:  P12643
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Bone morphogenetic protein receptor type IA
B, E
131Homo sapiensMutation(s): 0 
Gene Names: BMPR1A (ACVRLK3, ALK3)
EC: 2.7.11.30
Find proteins for P36894 (Homo sapiens)
Go to Gene View: BMPR1A
Go to UniProtKB:  P36894
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Activin receptor type 2A
C, F
102Mus musculusMutation(s): 0 
Gene Names: Acvr2a (Acvr2)
EC: 2.7.11.30
Find proteins for P27038 (Mus musculus)
Go to UniProtKB:  P27038
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDG
Query on NDG

Download SDF File 
Download CCD File 
C, F
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.222 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 104.031α = 90.00
b = 104.031β = 90.00
c = 362.526γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
REFMACrefinement
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-05-09
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Advisory, Refinement description