9DPY | pdb_00009dpy

BMP-10 with BMP-9 Crystal Contacts

  • Classification: SIGNALING PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2024-09-23 Released: 2025-03-05 
  • Deposition Author(s): Schwartze, T.A., Hinck, A.P.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Defense (DOD, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 
    0.251 (Depositor), 0.251 (DCC) 
  • R-Value Work: 
    0.214 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Molecular Basis of Interchain Disulfide Bond Formation in BMP-9 and BMP-10.

Schwartze, T.A.Morosky, S.A.Rosato, T.L.Henrickson, A.Lin, G.Hinck, C.S.Taylor, A.B.Olsen, S.K.Calero, G.Demeler, B.Roman, B.L.Hinck, A.P.

(2025) J Mol Biology 437: 168935-168935

  • DOI: https://doi.org/10.1016/j.jmb.2025.168935
  • Primary Citation of Related Structures:  
    9DPM, 9DPN, 9DPO, 9DPP, 9DPQ, 9DPR, 9DPS, 9DPT, 9DPU, 9DPV, 9DPW, 9DPX, 9DPY

  • PubMed Abstract: 

    BMP-9 and BMP-10 are TGF-β family signaling ligands naturally secreted into blood. They act on endothelial cells and are required for proper development and maintenance of the vasculature. In hereditary hemorrhagic telangiectasia, regulation is disrupted due to mutations in the BMP-9/10 pathway, namely in the type I receptor ALK1 or the co-receptor endoglin. It has been demonstrated that BMP-9/10 heterodimers are the most abundant signaling species in the blood, but it is unclear how they form. Unlike other ligands of the TGF-β family, BMP-9 and -10 are secreted as a mixture of disulfide-linked dimers and monomers, in which the interchain cysteine (Cys-392) remains either paired or unpaired. Here, we show that the monomers are secreted in a cysteinylated form that crystallizes as a non-covalent dimer. Despite this, monomers do not self-associate at micromolar or lower concentrations and have reduced signaling potency compared to disulfide-linked dimers. We further show using protein crystallography that the interchain disulfide of the BMP-9 homodimer adopts a highly strained syn-periplanar conformation. Hence, geometric strain across the interchain disulfide is responsible for infrequent interchain disulfide bond formation, not the cysteinylation. Additionally, we show that interchain disulfide bond formation occurs less in BMP-9 than BMP-10 and these frequencies can be reversed by swapping residues near the interchain disulfide that form attractive interactions with the opposing protomer. Finally, we discuss the implications of these observations on BMP-9/10 heterodimer formation.


  • Organizational Affiliation
    • Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bone morphogenetic protein 10
A, B
108Homo sapiensMutation(s): 5 
Gene Names: BMP10
UniProt & NIH Common Fund Data Resources
Find proteins for O95393 (Homo sapiens)
Explore O95393 
Go to UniProtKB:  O95393
PHAROS:  O95393
GTEx:  ENSG00000163217 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95393
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
NA
Query on NA

Download Ideal Coordinates CCD File 
I [auth A],
Q [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free:  0.251 (Depositor), 0.251 (DCC) 
  • R-Value Work:  0.214 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.752α = 90
b = 123.038β = 90
c = 120.558γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

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 StatesGM58670
Department of Defense (DOD, United States)United StatesW81XWH-17-1-0429

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release