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- PDB-2h64: Crystal structure of a ternary ligand-receptor complex of BMP-2 -

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Basic information

Entry
Database: PDB / ID: 2h64
TitleCrystal structure of a ternary ligand-receptor complex of BMP-2
Components
  • Acvr2b protein
  • Bone morphogenetic protein 2
  • Bone morphogenetic protein receptor type IA
KeywordsHormone/Growth Factor / TGF-beta superfamily / ligand-receptor complex / Hormone-Growth Factor COMPLEX
Function / homology
Function and homology information


Signaling by Activin / positive regulation of transforming growth factor beta2 production / positive regulation of cardiac ventricle development / fibrous ring of heart morphogenesis / inhibin binding / cardiac atrium formation / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / corticotropin hormone secreting cell differentiation / thyroid-stimulating hormone-secreting cell differentiation ...Signaling by Activin / positive regulation of transforming growth factor beta2 production / positive regulation of cardiac ventricle development / fibrous ring of heart morphogenesis / inhibin binding / cardiac atrium formation / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / corticotropin hormone secreting cell differentiation / thyroid-stimulating hormone-secreting cell differentiation / atrioventricular node cell development / cardiac jelly development / negative regulation of steroid biosynthetic process / activin receptor activity / negative regulation of aldosterone biosynthetic process / negative regulation of cortisol biosynthetic process / embryonic heart tube anterior/posterior pattern specification / positive regulation of extracellular matrix constituent secretion / atrioventricular canal morphogenesis / pericardium development / activin receptor activity, type II / lymphatic endothelial cell differentiation / mesenchymal cell proliferation involved in ureteric bud development / telencephalon regionalization / positive regulation of activin receptor signaling pathway / anti-Mullerian hormone receptor signaling pathway / Signaling by BMP / dorsal aorta morphogenesis / embryonic foregut morphogenesis / negative regulation of insulin-like growth factor receptor signaling pathway / lung vasculature development / tricuspid valve morphogenesis / negative regulation of cardiac muscle cell differentiation / positive regulation of odontogenesis / endodermal-mesodermal cell signaling / cardiac right ventricle morphogenesis / lymphangiogenesis / regulation of cardiac muscle cell proliferation / gastrulation with mouth forming second / aortic valve development / positive regulation of phosphatase activity / BMP binding / pharyngeal arch artery morphogenesis / positive regulation of cartilage development / retina vasculature development in camera-type eye / atrioventricular valve development / heart induction / venous blood vessel development / positive regulation of peroxisome proliferator activated receptor signaling pathway / mesenchyme development / trophoblast cell migration / mitral valve morphogenesis / BMP receptor complex / positive regulation of astrocyte differentiation / BMP receptor activity / organ growth / ventricular compact myocardium morphogenesis / cardiac conduction system development / negative regulation of smooth muscle cell migration / artery development / cardiac epithelial to mesenchymal transition / mesenchymal cell differentiation / transforming growth factor beta receptor activity, type I / positive regulation of bone mineralization involved in bone maturation / positive regulation of odontoblast differentiation / co-receptor binding / pattern specification process / telencephalon development / activin receptor complex / anterior/posterior pattern specification / Transcriptional regulation by RUNX2 / BMP receptor binding / phosphatase activator activity / endocardial cushion formation / receptor protein serine/threonine kinase / cellular response to BMP stimulus / cardiac muscle cell differentiation / activin binding / pancreas development / determination of left/right symmetry / transmembrane receptor protein serine/threonine kinase activity / cardiac muscle tissue morphogenesis / atrioventricular valve morphogenesis / Signaling by BMP / ventricular trabecula myocardium morphogenesis / activin receptor signaling pathway / negative regulation of ossification / dorsal/ventral pattern formation / outflow tract septum morphogenesis / skeletal system morphogenesis / endocardial cushion morphogenesis / odontogenesis of dentin-containing tooth / post-embryonic development / branching involved in ureteric bud morphogenesis / positive regulation of ossification / positive regulation of p38MAPK cascade / chondrocyte differentiation / insulin secretion / positive regulation of dendrite development / kinase activator activity
Similarity search - Function
: / GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / Activin types I and II receptor domain / Activin types I and II receptor domain / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site ...: / GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / Activin types I and II receptor domain / Activin types I and II receptor 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 / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / CD59 / CD59 / 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 / Ribbon / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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 / Activin receptor type-2B / Bone morphogenetic protein receptor type-1A / Activin receptor type-2B
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsMueller, T.D. / Sebald, W. / Weber, D.
CitationJournal: Bmc Struct.Biol. / Year: 2007
Title: A silent H-bond can be mutationally activated for high-affinity interaction of BMP-2 and activin type IIB receptor.
Authors: Weber, D. / Kotzsch, A. / Nickel, J. / Harth, S. / Seher, A. / Mueller, U. / Sebald, W. / Mueller, T.D.
History
DepositionMay 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 2
B: Bone morphogenetic protein receptor type IA
C: Acvr2b protein


Theoretical massNumber of molelcules
Total (without water)38,7903
Polymers38,7903
Non-polymers00
Water3,765209
1
A: Bone morphogenetic protein 2
B: Bone morphogenetic protein receptor type IA
C: Acvr2b protein

A: Bone morphogenetic protein 2
B: Bone morphogenetic protein receptor type IA
C: Acvr2b protein


Theoretical massNumber of molelcules
Total (without water)77,5796
Polymers77,5796
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Unit cell
Length a, b, c (Å)82.790, 82.790, 111.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe asymmetric unit contains half of the hexameric assembly. The biological unit can be obtained by applying the symmetry operation: y, x, -z+1

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Components

#1: Protein Bone morphogenetic protein 2 / BMP-2 / BMP-2A


Mass: 12940.861 Da / Num. of mol.: 1 / Mutation: L100K, N102D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMP2, BMP2A / Production host: Escherichia coli (E. coli) / References: UniProt: P12643
#2: Protein Bone morphogenetic protein receptor type IA / Serine/threonine-protein kinase receptor R5 / SKR5 / Activin receptor-like kinase 3 / ALK-3 / CD292 antigen


Mass: 14199.918 Da / Num. of mol.: 1 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMPR1A, ACVRLK3, ALK3 / Production host: Escherichia coli (E. coli)
References: UniProt: P36894, receptor protein serine/threonine kinase
#3: Protein Acvr2b protein / Activin receptor type IIB


Mass: 11648.771 Da / Num. of mol.: 1 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Acvr2b / Production host: Escherichia coli (E. coli) / References: UniProt: Q3KQI1, UniProt: P27040*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.83 Å3/Da / Density % sol: 56.58 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.75
Details: 30% PEG3350, 0.1M Tris-HCl pH 8.75, 0.2M NH4CH3COO, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 8, 2005 / Details: Osmic VariMax HR
RadiationMonochromator: Osmic VariMax HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.78→500 Å / Num. all: 42780 / Num. obs: 42606 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rsym value: 0.069 / Net I/σ(I): 12.6
Reflection shellResolution: 1.78→1.84 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 4140 / Rsym value: 0.514 / % possible all: 98.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
d*TREKdata reduction
PHASERphasing
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→500 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.264 1701 random
Rwork0.228 --
all0.232 34211 -
obs0.232 34058 -
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.29 Å
Luzzati sigma a0.5 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 1.92→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2295 0 0 209 2504
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.249
X-RAY DIFFRACTIONc_dihedral_angle_d24.307
X-RAY DIFFRACTIONc_improper_angle_d0.794

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