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- PDB-7ppa: High resolution structure of bone morphogenetic protein receptor ... -

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Basic information

Entry
Database: PDB / ID: 7ppa
TitleHigh resolution 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
KeywordsCYTOKINE / BMPRII BMP10 TGF-beta ligand and receptor Signalling complex
Function / homology
Function and homology information


semi-lunar valve development / atrial cardiac muscle tissue morphogenesis / regulation of cardiac muscle hypertrophy in response to stress / activin receptor activity, type II / negative regulation of chondrocyte proliferation / lymphatic endothelial cell differentiation / regulation of lung blood pressure / positive regulation of cell proliferation involved in heart morphogenesis / pulmonary valve development / positive regulation of sarcomere organization ...semi-lunar valve development / atrial cardiac muscle tissue morphogenesis / regulation of cardiac muscle hypertrophy in response to stress / activin receptor activity, type II / negative regulation of chondrocyte proliferation / lymphatic endothelial cell differentiation / regulation of lung blood pressure / positive regulation of cell proliferation involved in heart morphogenesis / pulmonary valve development / positive regulation of sarcomere organization / tricuspid valve morphogenesis / chondrocyte development / negative regulation of cell proliferation involved in heart valve morphogenesis / venous blood vessel development / aortic valve development / BMP binding / proteoglycan biosynthetic process / ventricular cardiac muscle cell development / negative regulation of muscle cell differentiation / atrial septum morphogenesis / endocardial cushion development / maternal placenta development / positive regulation of cartilage development / endochondral bone morphogenesis / transforming growth factor beta receptor activity / telethonin binding / lung vasculature development / lymphangiogenesis / mitral valve morphogenesis / negative regulation of cardiac muscle hypertrophy / BMP receptor activity / retina vasculature development in camera-type eye / positive regulation of axon extension involved in axon guidance / artery development / receptor protein serine/threonine kinase / Signaling by BMP / cellular response to BMP stimulus / activin receptor signaling pathway / endothelial cell apoptotic process / heart trabecula formation / receptor serine/threonine kinase binding / adult heart development / positive regulation of ossification / negative regulation of systemic arterial blood pressure / limb development / Molecules associated with elastic fibres / endothelial cell proliferation / negative regulation of endothelial cell migration / anterior/posterior pattern specification / cardiac muscle cell proliferation / ventricular cardiac muscle tissue morphogenesis / cell surface receptor protein serine/threonine kinase signaling pathway / negative regulation of vasoconstriction / sarcomere organization / ventricular septum morphogenesis / lung alveolus development / positive regulation of epithelial cell migration / positive regulation of cardiac muscle hypertrophy / blood vessel development / outflow tract morphogenesis / growth factor binding / positive regulation of SMAD protein signal transduction / mesoderm formation / regulation of cardiac muscle contraction / blood vessel remodeling / BMP signaling pathway / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / clathrin-coated pit / positive regulation of cardiac muscle cell proliferation / cellular response to starvation / negative regulation of cell migration / protein tyrosine kinase binding / basal plasma membrane / kidney development / cytokine activity / caveola / negative regulation of smooth muscle cell proliferation / adherens junction / growth factor activity / negative regulation of cell growth / hormone activity / cellular response to growth factor stimulus / Z disc / osteoblast differentiation / regulation of cell population proliferation / postsynaptic density / receptor complex / cell adhesion / cadherin binding / apical plasma membrane / phosphorylation / 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 / extracellular space
Similarity search - Function
TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Activin types I and II receptor domain / Activin types I and II receptor domain / 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. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Activin types I and II receptor domain / Activin types I and II receptor domain / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Cystine-knot cytokine / 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: 1.48 Å
AuthorsGuo, J. / Yu, M. / Read, R.J. / 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 / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bone morphogenetic protein 10
B: Bone morphogenetic protein 10
C: Bone morphogenetic protein receptor type-2
D: Bone morphogenetic protein receptor type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3775
Polymers52,2854
Non-polymers921
Water6,341352
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-48 kcal/mol
Surface area21660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.718, 47.228, 250.085
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32C
42D

NCS domain segments:

Beg auth comp-ID: ASN / Beg label comp-ID: ASN

Dom-IDComponent-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111CYSCYSAA321 - 4235 - 107
221CYSCYSBB321 - 4235 - 107
332PROPROCC29 - 1334 - 108
442LEULEUDD29 - 1394 - 114

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4

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Components

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


Mass: 12177.185 Da / Num. of mol.: 2
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.: 2
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.54 Å3/Da / Density % sol: 51.63 % / Description: Thick plate
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 14% PEG 3350 0.19 M Ammonium citrate dibasic 0.02 M Sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.91589 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91589 Å / Relative weight: 1
ReflectionResolution: 1.48→125.04 Å / Num. obs: 89787 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.032 / Rrim(I) all: 0.115 / Net I/σ(I): 11.2
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 11.7 % / Rmerge(I) obs: 1.85 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4320 / CC1/2: 0.59 / Rpim(I) all: 0.554 / Rrim(I) all: 1.933 / % possible all: 99.8

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Processing

Software
NameVersionClassification
DIALS1.14.5data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
REFMAC5.8.0267refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SF3, 2HLQ

6sf3

2hlq


Resolution: 1.48→125.04 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.66 / SU ML: 0.05 / Cross valid method: FREE R-VALUE / ESU R: 0.062 / ESU R Free: 0.064
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2066 4383 4.889 %
Rwork0.1646 85272 -
all0.167 --
obs-89655 99.886 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.737 Å2
Baniso -1Baniso -2Baniso -3
1--0.651 Å20 Å20 Å2
2---0.492 Å20 Å2
3---1.143 Å2
Refinement stepCycle: LAST / Resolution: 1.48→125.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3165 0 6 352 3523
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0133404
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173055
X-RAY DIFFRACTIONr_angle_refined_deg1.8711.6514655
X-RAY DIFFRACTIONr_angle_other_deg1.5481.587117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2145437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.47623.379145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.87415546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8141511
X-RAY DIFFRACTIONr_chiral_restr0.1070.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024414
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02737
X-RAY DIFFRACTIONr_nbd_refined0.2290.2630
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.22709
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21606
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21575
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.090.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2240.228
X-RAY DIFFRACTIONr_nbd_other0.2040.298
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2690.231
X-RAY DIFFRACTIONr_mcbond_it7.1943.3181718
X-RAY DIFFRACTIONr_mcbond_other7.1963.3151717
X-RAY DIFFRACTIONr_mcangle_it7.6814.932159
X-RAY DIFFRACTIONr_mcangle_other7.684.9342160
X-RAY DIFFRACTIONr_scbond_it10.3513.7391686
X-RAY DIFFRACTIONr_scbond_other10.3483.7411687
X-RAY DIFFRACTIONr_scangle_it10.4525.42494
X-RAY DIFFRACTIONr_scangle_other10.455.4022495
X-RAY DIFFRACTIONr_lrange_it9.7431.8023813
X-RAY DIFFRACTIONr_lrange_other9.7219125.3873727
X-RAY DIFFRACTIONr_rigid_bond_restr15.34232687
X-RAY DIFFRACTIONr_ncsr_local_group_10.1210.053208
X-RAY DIFFRACTIONr_ncsr_local_group_20.1830.052563
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.121230.05007
12BX-RAY DIFFRACTIONLocal ncs0.121230.05007
23CX-RAY DIFFRACTIONLocal ncs0.182930.05007
24DX-RAY DIFFRACTIONLocal ncs0.182930.05007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.5180.3013450.2616144X-RAY DIFFRACTION99.6774
1.518-1.560.2793370.256027X-RAY DIFFRACTION99.8275
1.56-1.6050.2623070.215904X-RAY DIFFRACTION99.8874
1.605-1.6550.222860.1815758X-RAY DIFFRACTION99.9835
1.655-1.7090.2572610.1755599X-RAY DIFFRACTION99.9659
1.709-1.7690.2212650.1645372X-RAY DIFFRACTION99.876
1.769-1.8360.2062660.1485183X-RAY DIFFRACTION99.9633
1.836-1.9110.1782840.1285040X-RAY DIFFRACTION99.9812
1.911-1.9960.1952310.1434810X-RAY DIFFRACTION99.9009
1.996-2.0930.1972440.1554626X-RAY DIFFRACTION100
2.093-2.2060.1951990.1574416X-RAY DIFFRACTION99.9783
2.206-2.340.1952170.1514197X-RAY DIFFRACTION99.9773
2.34-2.5020.1922320.1553933X-RAY DIFFRACTION99.952
2.502-2.7020.2161870.1693642X-RAY DIFFRACTION99.9217
2.702-2.960.2031750.1593447X-RAY DIFFRACTION99.8897
2.96-3.3090.1881500.1573063X-RAY DIFFRACTION99.9689
3.309-3.8210.1831340.1452767X-RAY DIFFRACTION99.8967
3.821-4.6790.1781090.1292368X-RAY DIFFRACTION99.9596
4.679-6.6160.2151010.1911865X-RAY DIFFRACTION100
6.616-125.040.275530.2681111X-RAY DIFFRACTION99.8285

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