7U5O

CRYSTAL STRUCTURE OF THE BONE MORPHOGENETIC PROTEIN RECEPTOR TYPE 2 LIGAND BINDING DOMAIN IN COMPLEX WITH ACTIVIN-B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.238 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Type II BMP and activin receptors BMPR2 and ACVR2A share a conserved mode of growth factor recognition.

Chu, K.Y.Malik, A.Thamilselvan, V.Martinez-Hackert, E.

(2022) J Biol Chem 298: 102076-102076

  • DOI: https://doi.org/10.1016/j.jbc.2022.102076
  • Primary Citation of Related Structures:  
    7U5O

  • PubMed Abstract: 

    BMPR2 is a type II Transforming Growth Factor (TGF)-β family receptor that is fundamentally associated with pulmonary arterial hypertension (PAH) in humans. BMPR2 shares functional similarities with the type II activin receptors ACVR2A and ACVR2B, as it interacts with an overlapping group of TGF-β family growth factors (GFs). However, how BMPR2 recognizes GFs remains poorly understood. Here, we solved crystal structures of BMPR2 in complex with the GF activin B and of ACVR2A in complex with the related GF activin A. We show that both BMPR2 and ACVR2A bind GFs with nearly identical geometry using a conserved hydrophobic hot spot, while differences in contacting residues are predominantly found in loop areas. Upon further exploration of the GF-binding spectrum of the two receptors, we found that although many GFs bind both receptors, the high-affinity BMPR2 GFs comprise BMP15, BMP10, and Nodal, whereas those of ACVR2A are activin A, activin B, and GDF11. Lastly, we evaluated GF-binding domain BMPR2 variants found in human PAH patients. We demonstrate that mutations within the GF-binding interface resulted in loss of GF binding, while mutations in loop areas allowed BMPR2 to retain the ability to bind cognate GFs with high affinity. In conclusion, the in vitro activities of BMPR2 variants and the crystal structures reported here indicate biochemically relevant complexes that explain how some GF-binding domain variants can lead to PAH.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inhibin beta B chain
A, B, C
115Homo sapiensMutation(s): 0 
Gene Names: INHBB
UniProt & NIH Common Fund Data Resources
Find proteins for P09529 (Homo sapiens)
Explore P09529 
Go to UniProtKB:  P09529
PHAROS:  P09529
GTEx:  ENSG00000163083 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09529
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Bone morphogenetic protein receptor type-2D [auth E],
E [auth F],
F [auth G]
111Homo sapiensMutation(s): 0 
Gene Names: BMPR2PPH1
EC: 2.7.11.30
UniProt & NIH Common Fund Data Resources
Find proteins for Q13873 (Homo sapiens)
Explore Q13873 
Go to UniProtKB:  Q13873
PHAROS:  Q13873
GTEx:  ENSG00000204217 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13873
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.238 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.96α = 90
b = 115.46β = 100.92
c = 110.16γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM121499

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-22
    Type: Initial release
  • Version 1.1: 2022-07-06
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description