6UNP | pdb_00006unp

Crystal structure of the kinase domain of BMPR2-D485G


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.211 (Depositor), 0.194 (DCC) 
  • R-Value Work: 
    0.189 (Depositor) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structural basis for ALK2/BMPR2 receptor complex signaling through kinase domain oligomerization.

Agnew, C.Ayaz, P.Kashima, R.Loving, H.S.Ghatpande, P.Kung, J.E.Underbakke, E.S.Shan, Y.Shaw, D.E.Hata, A.Jura, N.

(2021) Nat Commun 12: 4950-4950

  • DOI: https://doi.org/10.1038/s41467-021-25248-5
  • Primary Citation Related Structures: 
    6UNP, 6UNQ, 6UNR, 6UNS

  • PubMed Abstract: 

    Upon ligand binding, bone morphogenetic protein (BMP) receptors form active tetrameric complexes, comprised of two type I and two type II receptors, which then transmit signals to SMAD proteins. The link between receptor tetramerization and the mechanism of kinase activation, however, has not been elucidated. Here, using hydrogen deuterium exchange mass spectrometry (HDX-MS), small angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations, combined with analysis of SMAD signaling, we show that the kinase domain of the type I receptor ALK2 and type II receptor BMPR2 form a heterodimeric complex via their C-terminal lobes. Formation of this dimer is essential for ligand-induced receptor signaling and is targeted by mutations in BMPR2 in patients with pulmonary arterial hypertension (PAH). We further show that the type I/type II kinase domain heterodimer serves as the scaffold for assembly of the active tetrameric receptor complexes to enable phosphorylation of the GS domain and activation of SMADs.


  • Organizational Affiliation
    • Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA.

Macromolecule Content 

  • Total Structure Weight: 85.83 kDa 
  • Atom Count: 4,994 
  • Modeled Residue Count: 605 
  • Deposited Residue Count: 726 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bone morphogenetic protein receptor type-2
A, B
363Homo sapiensMutation(s): 1 
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
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP

Query on ADP



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
P [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
BA [auth B],
CA [auth B],
L [auth A],
M [auth A],
N [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
DA [auth B],
EA [auth B],
O [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
AA [auth B]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
AA [auth B],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CAS
Query on CAS
A, B
L-PEPTIDE LINKINGC5 H12 As N O2 SCYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.211 (Depositor), 0.194 (DCC) 
  • R-Value Work:  0.189 (Depositor) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.497α = 90
b = 138.497β = 90
c = 109.992γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-07
    Type: Initial release
  • Version 1.1: 2021-10-13
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary