6SF2 | pdb_00006sf2

Ternary complex of human bone morphogenetic protein 9 (BMP9) growth factor domain, its prodomain and extracellular domain of activin receptor-like kinase 1 (ALK1).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.274 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.243 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.244 (Depositor) 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

Molecular basis of ALK1-mediated signalling by BMP9/BMP10 and their prodomain-bound forms.

Salmon, R.M.Guo, J.Wood, J.H.Tong, Z.Beech, J.S.Lawera, A.Yu, M.Grainger, D.J.Reckless, J.Morrell, N.W.Li, W.

(2020) Nat Commun 11: 1621-1621

  • DOI: https://doi.org/10.1038/s41467-020-15425-3
  • Primary Citation of Related Structures:  
    6SF1, 6SF2, 6SF3

  • PubMed Abstract: 

    Activin receptor-like kinase 1 (ALK1)-mediated endothelial cell signalling in response to bone morphogenetic protein 9 (BMP9) and BMP10 is of significant importance in cardiovascular disease and cancer. However, detailed molecular mechanisms of ALK1-mediated signalling remain unclear. Here, we report crystal structures of the BMP10:ALK1 complex at 2.3 Å and the prodomain-bound BMP9:ALK1 complex at 3.3 Å. Structural analyses reveal a tripartite recognition mechanism that defines BMP9 and BMP10 specificity for ALK1, and predict that crossveinless 2 is not an inhibitor of BMP9, which is confirmed by experimental evidence. Introduction of BMP10-specific residues into BMP9 yields BMP10-like ligands with diminished signalling activity in C2C12 cells, validating the tripartite mechanism. The loss of osteogenic signalling in C2C12 does not translate into non-osteogenic activity in vivo and BMP10 also induces bone-formation. Collectively, these data provide insight into ALK1-mediated BMP9 and BMP10 signalling, facilitating therapeutic targeting of this important pathway.


  • Organizational Affiliation

    The Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase receptor R3
A, D
98Homo sapiensMutation(s): 0 
Gene Names: ACVRL1ACVRLK1ALK1
EC: 2.7.11.30
UniProt & NIH Common Fund Data Resources
Find proteins for P37023 (Homo sapiens)
Explore P37023 
Go to UniProtKB:  P37023
PHAROS:  P37023
GTEx:  ENSG00000139567 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37023
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Growth/differentiation factor 2
B, E
110Homo sapiensMutation(s): 0 
Gene Names: GDF2BMP9
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UK05 (Homo sapiens)
Explore Q9UK05 
Go to UniProtKB:  Q9UK05
PHAROS:  Q9UK05
GTEx:  ENSG00000263761 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UK05
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Growth/differentiation factor 2
C, F
297Homo sapiensMutation(s): 0 
Gene Names: GDF2BMP9
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UK05 (Homo sapiens)
Explore Q9UK05 
Go to UniProtKB:  Q9UK05
PHAROS:  Q9UK05
GTEx:  ENSG00000263761 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UK05
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q9UK05-1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free:  0.274 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.243 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.244 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.61α = 90
b = 72.61β = 90
c = 438.485γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
British Heart FoundationUnited KingdomPG/12/54/29734
British Heart FoundationUnited KingdomPG/15/39/31519
British Heart FoundationUnited KingdomPG/17/1/32532

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-08
    Type: Initial release
  • Version 1.1: 2020-04-15
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.4: 2024-11-20
    Changes: Structure summary