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- PDB-7u5o: CRYSTAL STRUCTURE OF THE BONE MORPHOGENETIC PROTEIN RECEPTOR TYPE... -

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Basic information

Entry
Database: PDB / ID: 7u5o
TitleCRYSTAL STRUCTURE OF THE BONE MORPHOGENETIC PROTEIN RECEPTOR TYPE 2 LIGAND BINDING DOMAIN IN COMPLEX WITH ACTIVIN-B
Components
  • Bone morphogenetic protein receptor type-2
  • Inhibin beta B chain
KeywordsSIGNALING PROTEIN / Cell Signaling / Receptor-ligand complex / Growth factor / Receptor interaction / Activin B / BMPRII
Function / homology
Function and homology information


negative regulation of hepatocyte growth factor production / response to gonadotropin / semi-lunar valve development / positive regulation of ovulation / negative regulation of follicle-stimulating hormone secretion / negative regulation of chondrocyte proliferation / Antagonism of Activin by Follistatin / regulation of lung blood pressure / activin receptor activity, type II / lymphatic endothelial cell differentiation ...negative regulation of hepatocyte growth factor production / response to gonadotropin / semi-lunar valve development / positive regulation of ovulation / negative regulation of follicle-stimulating hormone secretion / negative regulation of chondrocyte proliferation / Antagonism of Activin by Follistatin / regulation of lung blood pressure / activin receptor activity, type II / lymphatic endothelial cell differentiation / pulmonary valve development / Glycoprotein hormones / chondrocyte development / tricuspid valve morphogenesis / negative regulation of cell proliferation involved in heart valve morphogenesis / aortic valve development / positive regulation of follicle-stimulating hormone secretion / BMP binding / atrial septum morphogenesis / negative regulation of muscle cell differentiation / venous blood vessel development / proteoglycan biosynthetic process / maternal placenta development / endochondral bone morphogenesis / positive regulation of cartilage development / endocardial cushion development / transforming growth factor beta receptor activity / pituitary gland development / lymphangiogenesis / mitral valve morphogenesis / BMP receptor activity / retina vasculature development in camera-type eye / positive regulation of axon extension involved in axon guidance / lung vasculature development / artery development / cellular response to cholesterol / receptor protein serine/threonine kinase / cellular response to BMP stimulus / Signaling by BMP / Signaling by Activin / oocyte development / activin receptor signaling pathway / cellular response to leptin stimulus / endothelial cell apoptotic process / response to insecticide / negative regulation of systemic arterial blood pressure / positive regulation of ossification / cellular response to thyroid hormone stimulus / endothelial cell proliferation / limb development / anterior/posterior pattern specification / cell surface receptor protein serine/threonine kinase signaling pathway / negative regulation of vasoconstriction / lung alveolus development / growth factor binding / ventricular septum morphogenesis / blood vessel development / seminiferous tubule development / fat cell differentiation / outflow tract morphogenesis / cellular response to Thyroglobulin triiodothyronine / mesoderm formation / positive regulation of SMAD protein signal transduction / positive regulation of epithelial cell migration / cellular response to interleukin-1 / blood vessel remodeling / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / BMP signaling pathway / ovarian follicle development / clathrin-coated pit / cellular response to calcium ion / protein tyrosine kinase binding / basal plasma membrane / cellular response to cAMP / cellular response to starvation / cytokine activity / positive regulation of apoptotic signaling pathway / cell periphery / adherens junction / stem cell differentiation / growth factor activity / apoptotic signaling pathway / negative regulation of smooth muscle cell proliferation / negative regulation of insulin secretion / defense response / negative regulation of cell growth / hormone activity / caveola / cellular response to growth factor stimulus / response to wounding / cellular response to insulin stimulus / osteoblast differentiation / regulation of cell population proliferation / spermatogenesis / cell differentiation / receptor complex / postsynaptic density / host cell surface receptor binding / apical plasma membrane
Similarity search - Function
Inhibin, beta B subunit / 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 ...Inhibin, beta B subunit / 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
Inhibin beta B chain / Bone morphogenetic protein receptor type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsChu, K.Y. / Malik, A. / Thamilselvan, V. / Martinez-Hackert, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM121499 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Type II BMP and activin receptors BMPR2 and ACVR2A share a conserved mode of growth factor recognition.
Authors: Chu, K.Y. / Malik, A. / Thamilselvan, V. / Martinez-Hackert, E.
History
DepositionMar 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
Revision 1.3Nov 20, 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: Inhibin beta B chain
B: Inhibin beta B chain
C: Inhibin beta B chain
E: Bone morphogenetic protein receptor type-2
F: Bone morphogenetic protein receptor type-2
G: Bone morphogenetic protein receptor type-2


Theoretical massNumber of molelcules
Total (without water)75,7606
Polymers75,7606
Non-polymers00
Water00
1
A: Inhibin beta B chain
E: Bone morphogenetic protein receptor type-2


Theoretical massNumber of molelcules
Total (without water)25,2532
Polymers25,2532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Inhibin beta B chain
F: Bone morphogenetic protein receptor type-2


Theoretical massNumber of molelcules
Total (without water)25,2532
Polymers25,2532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Inhibin beta B chain
G: Bone morphogenetic protein receptor type-2


Theoretical massNumber of molelcules
Total (without water)25,2532
Polymers25,2532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.960, 115.460, 110.160
Angle α, β, γ (deg.)90.000, 100.920, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 293 through 298 or (resid 299...
21(chain B and (resid 293 through 300 or (resid 301...
31(chain C and (resid 293 through 298 or (resid 299...
12(chain E and (resid 32 through 39 or (resid 40...
22(chain F and ((resid 32 through 33 and (name N...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYGLYGLY(chain A and (resid 293 through 298 or (resid 299...AA293 - 2981 - 6
121ARGARGARGARG(chain A and (resid 293 through 298 or (resid 299...AA2997
131GLYGLYALAALA(chain A and (resid 293 through 298 or (resid 299...AA293 - 4071 - 115
141GLYGLYALAALA(chain A and (resid 293 through 298 or (resid 299...AA293 - 4071 - 115
151GLYGLYALAALA(chain A and (resid 293 through 298 or (resid 299...AA293 - 4071 - 115
161GLYGLYALAALA(chain A and (resid 293 through 298 or (resid 299...AA293 - 4071 - 115
211GLYGLYTHRTHR(chain B and (resid 293 through 300 or (resid 301...BB293 - 3001 - 8
221ASNASNASNASN(chain B and (resid 293 through 300 or (resid 301...BB3019
231GLYGLYALAALA(chain B and (resid 293 through 300 or (resid 301...BB293 - 4071 - 115
241GLYGLYALAALA(chain B and (resid 293 through 300 or (resid 301...BB293 - 4071 - 115
251GLYGLYALAALA(chain B and (resid 293 through 300 or (resid 301...BB293 - 4071 - 115
261GLYGLYALAALA(chain B and (resid 293 through 300 or (resid 301...BB293 - 4071 - 115
311GLYGLYGLYGLY(chain C and (resid 293 through 298 or (resid 299...CC293 - 2981 - 6
321ARGARGARGARG(chain C and (resid 293 through 298 or (resid 299...CC2997
112ARGARGPROPRO(chain E and (resid 32 through 39 or (resid 40...ED32 - 396 - 13
122TYRTYRGLUGLU(chain E and (resid 32 through 39 or (resid 40...ED40 - 5414 - 28
132GLUGLUPROPRO(chain E and (resid 32 through 39 or (resid 40...ED31 - 1335 - 107
142GLUGLUPROPRO(chain E and (resid 32 through 39 or (resid 40...ED31 - 1335 - 107
152GLUGLUPROPRO(chain E and (resid 32 through 39 or (resid 40...ED31 - 1335 - 107
162GLUGLUPROPRO(chain E and (resid 32 through 39 or (resid 40...ED31 - 1335 - 107
212ARGARGLEULEU(chain F and ((resid 32 through 33 and (name N...FE32 - 336 - 7
222ARGARGPROPRO(chain F and ((resid 32 through 33 and (name N...FE32 - 1336 - 107
232ARGARGPROPRO(chain F and ((resid 32 through 33 and (name N...FE32 - 1336 - 107

NCS ensembles :
ID
1
2

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Components

#1: Protein Inhibin beta B chain / Activin beta-B chain


Mass: 12825.582 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INHBB / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P09529
#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: 12427.736 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMPR2, PPH1 / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: Q13873, receptor protein serine/threonine kinase
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: 3.34 Å3/Da / Density % sol: 58.81 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 175 mM Ammonium Sulfate 100 mM Bis Tris 14% PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.45→60.34 Å / Num. obs: 13152 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 112.69 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.062 / Rrim(I) all: 0.12 / Χ2: 0.57 / Net I/σ(I): 3
Reflection shellResolution: 3.45→3.78 Å / Num. unique obs: 3121 / CC1/2: 0.909 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HLR

2hlr


Resolution: 3.45→36.06 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2844 646 4.93 %
Rwork0.2357 12469 -
obs0.2381 13115 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 326.84 Å2 / Biso mean: 141.7258 Å2 / Biso min: 53.54 Å2
Refinement stepCycle: final / Resolution: 3.45→36.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4358 0 0 0 4358
Num. residues----587
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A975X-RAY DIFFRACTION10.949TORSIONAL
12B975X-RAY DIFFRACTION10.949TORSIONAL
13C975X-RAY DIFFRACTION10.949TORSIONAL
21E414X-RAY DIFFRACTION10.949TORSIONAL
22F414X-RAY DIFFRACTION10.949TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.45-3.720.29411320.263224882620100
3.72-4.090.32111240.22524922616100
4.09-4.680.26841250.197624972622100
4.68-5.890.26141330.232725092642100
5.89-36.060.29311320.25462483261598
Refinement TLS params.Method: refined / Origin x: 1.4519 Å / Origin y: -32.9811 Å / Origin z: 36.0131 Å
111213212223313233
T0.8649 Å2-0.0828 Å20.1325 Å2-0.7163 Å20.0568 Å2--0.7755 Å2
L1.3553 °2-0.0664 °2-0.6714 °2-1.6416 °20.4342 °2--1.3907 °2
S-0.1986 Å °0.2911 Å °-0.0021 Å °-0.5955 Å °0.0989 Å °-0.4153 Å °-0.0125 Å °0.1515 Å °0.1242 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA293 - 407
2X-RAY DIFFRACTION1allB293 - 407
3X-RAY DIFFRACTION1allC293 - 407
4X-RAY DIFFRACTION1allE31 - 133
5X-RAY DIFFRACTION1allF32 - 133
6X-RAY DIFFRACTION1allG30 - 131

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