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- PDB-1es7: COMPLEX BETWEEN BMP-2 AND TWO BMP RECEPTOR IA ECTODOMAINS -

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Basic information

Entry
Database: PDB / ID: 1es7
TitleCOMPLEX BETWEEN BMP-2 AND TWO BMP RECEPTOR IA ECTODOMAINS
Components
  • BONE MORPHOGENETIC PROTEIN RECEPTOR IA
  • BONE MORPHOGENETIC PROTEIN-2
KeywordsCYTOKINE / protein-protein complex / three finger toxin fold / receptor-ligand complex / cytokine receptor / TGF beta superfamily
Function / homology
Function and homology information


neural plate mediolateral regionalization / paraxial mesoderm structural organization / positive regulation of cardiac ventricle development / fibrous ring of heart morphogenesis / positive regulation of transforming growth factor beta2 production / cardiac atrium formation / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / Mullerian duct regression / heart formation ...neural plate mediolateral regionalization / paraxial mesoderm structural organization / positive regulation of cardiac ventricle development / fibrous ring of heart morphogenesis / positive regulation of transforming growth factor beta2 production / cardiac atrium formation / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / Mullerian duct regression / heart formation / cardiac jelly development / atrioventricular node cell development / negative regulation of aldosterone biosynthetic process / negative regulation of cortisol biosynthetic process / atrioventricular canal morphogenesis / mesenchymal cell proliferation involved in ureteric bud development / negative regulation of steroid biosynthetic process / embryonic heart tube anterior/posterior pattern specification / mesendoderm development / positive regulation of extracellular matrix constituent secretion / dorsal aorta morphogenesis / regulation of odontogenesis of dentin-containing tooth / tricuspid valve morphogenesis / endodermal-mesodermal cell signaling / negative regulation of cardiac muscle cell differentiation / corticotropin hormone secreting cell differentiation / central nervous system neuron differentiation / negative regulation of insulin-like growth factor receptor signaling pathway / atrioventricular valve development / thyroid-stimulating hormone-secreting cell differentiation / cardiac right ventricle morphogenesis / positive regulation of phosphatase activity / mesenchyme development / aortic valve development / ameloblast differentiation / telencephalon regionalization / BMP binding / hindlimb morphogenesis / negative regulation of muscle cell differentiation / regulation of cardiac muscle cell proliferation / pharyngeal arch artery morphogenesis / heart induction / positive regulation of odontogenesis / positive regulation of cartilage development / positive regulation of peroxisome proliferator activated receptor signaling pathway / regulation of lateral mesodermal cell fate specification / lateral mesoderm development / pituitary gland development / ventricular compact myocardium morphogenesis / pericardium development / lung vasculature development / mitral valve morphogenesis / BMP receptor complex / negative regulation of smooth muscle cell migration / co-receptor binding / regulation of cellular senescence / proteoglycan metabolic process / dorsal/ventral axis specification / neural crest cell development / ectoderm development / cardiac epithelial to mesenchymal transition / mesenchymal cell differentiation / telencephalon development / BMP receptor binding / cardiac conduction system development / positive regulation of odontoblast differentiation / positive regulation of bone mineralization involved in bone maturation / Transcriptional regulation by RUNX2 / endocardial cushion formation / phosphatase activator activity / positive regulation of astrocyte differentiation / transforming growth factor beta receptor activity, type I / activin receptor activity, type I / activin receptor activity, type II / BMP receptor activity / receptor protein serine/threonine kinase / transforming growth factor beta receptor activity, type II / transmembrane receptor protein serine/threonine kinase activity / transforming growth factor beta receptor activity, type III / cellular response to BMP stimulus / cardiac muscle cell differentiation / Signaling by BMP / ventricular trabecula myocardium morphogenesis / cardiac muscle tissue morphogenesis / outflow tract septum morphogenesis / astrocyte differentiation / positive regulation of ossification / dorsal/ventral pattern formation / positive regulation of p38MAPK cascade / atrioventricular valve morphogenesis / positive regulation of dendrite development / positive regulation of mesenchymal cell proliferation / endocardial cushion morphogenesis / Molecules associated with elastic fibres / branching involved in ureteric bud morphogenesis / embryonic digit morphogenesis / ventricular septum morphogenesis / negative regulation of fat cell differentiation / roof of mouth development / bone mineralization
Similarity search - Function
: / GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / TGF-beta, propeptide / TGF-beta propeptide / Activin types I and II receptor domain / Activin types I and II receptor domain / Transforming growth factor beta, conserved site ...: / GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / TGF-beta, propeptide / TGF-beta propeptide / Activin types I and II receptor domain / Activin types I and II receptor domain / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Cystine-knot cytokine / Snake toxin-like superfamily / Ribbon / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Bone morphogenetic protein 2 / Bone morphogenetic protein receptor type-1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsKirsch, T. / Sebald, W. / Dreyer, M.K.
Citation
Journal: Nat.Struct.Biol. / Year: 2000
Title: Crystal structure of the BMP-2-BRIA ectodomain complex.
Authors: Kirsch, T. / Sebald, W. / Dreyer, M.K.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Crystal Structure of Human Bone Morphogenetic Protein-2 at 2.7 A Resolution
Authors: Scheufler, C. / Sebald, W. / Hulsmeyer, M.
#2: Journal: FEBS Lett. / Year: 2000
Title: Isolation of Recombinant BMP Receptor IA Ectodomain and its 2:1 Complex with BMP-2
Authors: Kirsch, T. / Nickel, J. / Sebald, W.
History
DepositionApr 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.6Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BONE MORPHOGENETIC PROTEIN-2
B: BONE MORPHOGENETIC PROTEIN RECEPTOR IA
C: BONE MORPHOGENETIC PROTEIN-2
D: BONE MORPHOGENETIC PROTEIN RECEPTOR IA


Theoretical massNumber of molelcules
Total (without water)46,0574
Polymers46,0574
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-46 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.330, 109.330, 101.905
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsThe biological assembly is constructed from all four chains in the asymmetric unit and contains one covalently linked BMP-2 dimer and two receptor chains

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Components

#1: Protein BONE MORPHOGENETIC PROTEIN-2 / BMP-2


Mass: 13126.128 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: RBSIIP / Production host: Escherichia coli (E. coli) / References: UniProt: P12643
#2: Protein BONE MORPHOGENETIC PROTEIN RECEPTOR IA / ALK-3


Mass: 9902.242 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET32A / Production host: Escherichia coli (E. coli)
References: UniProt: P36894, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 3.2 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: sodium acetate, imidazole, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
220 mMMES1drop
30.7 M1dropNaCl
40.75 Msodium acetate1reservoir
50.1 mMimidazole1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS X1000 / Detector: AREA DETECTOR / Date: Aug 12, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→16 Å / Num. all: 52517 / Num. obs: 57236 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.45 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 10.2
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1467 / % possible all: 99.5
Reflection
*PLUS
Num. obs: 15184
Reflection shell
*PLUS
% possible obs: 99.5 %

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Processing

Software
NameVersionClassification
FRAMBOdata collection
XDSdata reduction
AMoREphasing
CNS0.9refinement
XDSdata scaling
RefinementResolution: 2.9→100 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 1519 10 %random
Rwork0.1905 ---
all-15416 --
obs-15184 9.9 %-
Displacement parametersBiso mean: 40 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati sigma a0.47 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.9→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2930 0 0 82 3012
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006855
X-RAY DIFFRACTIONc_angle_deg1.31301
X-RAY DIFFRACTIONc_dihedral_angle_d25.05
X-RAY DIFFRACTIONc_improper_angle_d0.89
LS refinement shellResolution: 2.9→3 Å /
Rfactor% reflection
Rfree0.3 -
Rwork0.278 -
obs-99.5 %
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.05
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89

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