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- PDB-7ppb: 2.4 angstrom crystal structure of bone morphogenetic protein rece... -

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Basic information

Entry
Database: PDB / ID: 7ppb
Title2.4 angstrom crystal structure of bone morphogenetic protein receptor type II (BMPRII) extracellular domain in complex with BMP10
Components
  • Bone morphogenetic protein 10
  • Bone morphogenetic protein receptor type-2
KeywordsSIGNALING PROTEIN / BMPRII BMP10 TGF-beta ligand and receptor Signalling complex
Function / homology
Function and homology information


semi-lunar valve development / negative regulation of chondrocyte proliferation / regulation of cardiac muscle hypertrophy in response to stress / regulation of lung blood pressure / activin receptor activity, type II / lymphatic endothelial cell differentiation / pulmonary valve development / chondrocyte development / positive regulation of sarcomere organization / tricuspid valve morphogenesis ...semi-lunar valve development / negative regulation of chondrocyte proliferation / regulation of cardiac muscle hypertrophy in response to stress / regulation of lung blood pressure / activin receptor activity, type II / lymphatic endothelial cell differentiation / pulmonary valve development / chondrocyte development / positive regulation of sarcomere organization / tricuspid valve morphogenesis / positive regulation of cell proliferation involved in heart morphogenesis / atrial cardiac muscle tissue morphogenesis / negative regulation of cell proliferation involved in heart valve morphogenesis / aortic valve development / BMP binding / atrial septum morphogenesis / negative regulation of muscle cell differentiation / venous blood vessel development / proteoglycan biosynthetic process / maternal placenta development / ventricular cardiac muscle cell development / endochondral bone morphogenesis / positive regulation of cartilage development / endocardial cushion development / telethonin binding / transforming growth factor beta receptor activity / lymphangiogenesis / mitral valve morphogenesis / BMP receptor activity / retina vasculature development in camera-type eye / negative regulation of cardiac muscle hypertrophy / positive regulation of axon extension involved in axon guidance / lung vasculature development / artery development / receptor protein serine/threonine kinase / cellular response to BMP stimulus / Signaling by BMP / activin receptor signaling pathway / endothelial cell apoptotic process / receptor serine/threonine kinase binding / adult heart development / heart trabecula formation / negative regulation of systemic arterial blood pressure / positive regulation of ossification / endothelial cell proliferation / limb development / negative regulation of endothelial cell migration / anterior/posterior pattern specification / cell surface receptor protein serine/threonine kinase signaling pathway / sarcomere organization / Molecules associated with elastic fibres / negative regulation of vasoconstriction / lung alveolus development / growth factor binding / ventricular cardiac muscle tissue morphogenesis / ventricular septum morphogenesis / positive regulation of cardiac muscle hypertrophy / blood vessel development / outflow tract morphogenesis / mesoderm formation / positive regulation of SMAD protein signal transduction / positive regulation of epithelial cell migration / blood vessel remodeling / regulation of cardiac muscle contraction / cardiac muscle cell proliferation / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / BMP signaling pathway / positive regulation of cardiac muscle cell proliferation / clathrin-coated pit / protein tyrosine kinase binding / basal plasma membrane / negative regulation of cell migration / cellular response to starvation / cytokine activity / adherens junction / stem cell differentiation / growth factor activity / kidney development / negative regulation of smooth muscle cell proliferation / negative regulation of cell growth / hormone activity / caveola / cellular response to growth factor stimulus / Z disc / osteoblast differentiation / regulation of cell population proliferation / cell differentiation / receptor complex / cell adhesion / postsynaptic density / apical plasma membrane / cadherin binding / axon / neuronal cell body / dendrite / positive regulation of gene expression / positive regulation of DNA-templated transcription / cell surface / positive regulation of transcription by RNA polymerase II
Similarity search - Function
TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Activin types I and II receptor domain / Transforming growth factor-beta-related / Activin types I and II receptor domain / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain ...TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Activin types I and II receptor domain / Transforming growth factor-beta-related / Activin types I and II receptor domain / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Ser/Thr protein kinase, TGFB receptor / Cystine-knot cytokine / Snake toxin-like superfamily / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Bone morphogenetic protein 10 / Bone morphogenetic protein receptor type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGuo, J. / Yu, M. / Li, W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
British Heart FoundationPG/12/54/29734, PG/17/1/32532, FS/SBSRF/20/31005 United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Crystal structures of BMPRII extracellular domain in binary and ternary receptor complexes with BMP10.
Authors: Guo, J. / Liu, B. / Thorikay, M. / Yu, M. / Li, X. / Tong, Z. / Salmon, R.M. / Read, R.J. / Ten Dijke, P. / Morrell, N.W. / Li, W.
History
DepositionSep 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bone morphogenetic protein 10
B: Bone morphogenetic protein receptor type-2


Theoretical massNumber of molelcules
Total (without water)26,1432
Polymers26,1432
Non-polymers00
Water68538
1
A: Bone morphogenetic protein 10
B: Bone morphogenetic protein receptor type-2

A: Bone morphogenetic protein 10
B: Bone morphogenetic protein receptor type-2


Theoretical massNumber of molelcules
Total (without water)52,2854
Polymers52,2854
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area6600 Å2
ΔGint-53 kcal/mol
Surface area20060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.589, 46.343, 43.753
Angle α, β, γ (deg.)90.000, 110.574, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Bone morphogenetic protein 10 / BMP-10


Mass: 12177.185 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMP10 / Cell line (production host): HEK EBNA / Production host: Homo sapiens (human) / References: UniProt: O95393
#2: Protein Bone morphogenetic protein receptor type-2 / BMP type-2 receptor / BMPR-2 / Bone morphogenetic protein receptor type II / BMP type II receptor / BMPR-II


Mass: 13965.368 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMPR2, PPH1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q13873, receptor protein serine/threonine kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 14% PEG 3350 0.14 M KCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→42.82 Å / Num. obs: 8820 / % possible obs: 99 % / Redundancy: 6.9 % / Biso Wilson estimate: 35.96 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.217 / Rpim(I) all: 0.089 / Rrim(I) all: 0.234 / Net I/σ(I): 6.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.048 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 887 / CC1/2: 0.745 / Rpim(I) all: 0.508 / Rrim(I) all: 1.284 / % possible all: 96.3

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Processing

Software
NameVersionClassification
autoPROCdata processing
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIX1.19.2_4158refinement
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PPA

7ppa


Resolution: 2.4→42.82 Å / SU ML: 0.3479 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.5009
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2347 438 4.98 %
Rwork0.2061 8361 -
obs0.2076 8799 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.42 Å2
Refinement stepCycle: LAST / Resolution: 2.4→42.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1564 0 0 38 1602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00231604
X-RAY DIFFRACTIONf_angle_d0.61842175
X-RAY DIFFRACTIONf_chiral_restr0.0412234
X-RAY DIFFRACTIONf_plane_restr0.0047278
X-RAY DIFFRACTIONf_dihedral_angle_d16.807586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.750.29871490.27222728X-RAY DIFFRACTION97.62
2.75-3.460.24631190.22822792X-RAY DIFFRACTION98.71
3.46-42.820.21031700.17752841X-RAY DIFFRACTION99.08
Refinement TLS params.Method: refined / Origin x: -27.0589423588 Å / Origin y: 17.0557902789 Å / Origin z: 15.5973021841 Å
111213212223313233
T0.425685514444 Å20.0216837906363 Å2-0.220453102002 Å2-0.301674334443 Å20.00354469198512 Å2--0.373628683828 Å2
L4.85379057296 °21.66242463375 °22.34839611191 °2-0.842909337559 °21.04926800454 °2--1.72106098934 °2
S0.0549329805252 Å °-0.0695366042463 Å °-0.0744213589517 Å °-0.0370136033614 Å °-0.0601312529372 Å °0.0698807401763 Å °0.00382942047666 Å °-0.120738698331 Å °0.0164812658279 Å °
Refinement TLS groupSelection details: all

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