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- PDB-2goo: Ternary Complex of BMP-2 bound to BMPR-Ia-ECD and ActRII-ECD -

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Basic information

Entry
Database: PDB / ID: 2goo
TitleTernary Complex of BMP-2 bound to BMPR-Ia-ECD and ActRII-ECD
Components
  • Activin receptor type 2A
  • Bone morphogenetic protein 2
  • Bone morphogenetic protein receptor type IA
KeywordsTRANSFERASE / TGF-beta / BMP-2 / BMPR-Ia / ActRII / ALK-3
Function / homology
Function and homology information


Signaling by Activin / neural plate mediolateral regionalization / paraxial mesoderm structural organization / positive regulation of cardiac ventricle development / fibrous ring of heart morphogenesis / inhibin-betaglycan-ActRII complex / positive regulation of transforming growth factor beta2 production / inhibin binding / Mullerian duct regression / Signaling by BMP ...Signaling by Activin / neural plate mediolateral regionalization / paraxial mesoderm structural organization / positive regulation of cardiac ventricle development / fibrous ring of heart morphogenesis / inhibin-betaglycan-ActRII complex / positive regulation of transforming growth factor beta2 production / inhibin binding / Mullerian duct regression / Signaling by BMP / cardiac atrium formation / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / cardiac jelly development / heart formation / atrioventricular node cell development / negative regulation of aldosterone biosynthetic process / embryonic heart tube anterior/posterior pattern specification / atrioventricular canal morphogenesis / negative regulation of cortisol biosynthetic process / penile erection / mesenchymal cell proliferation involved in ureteric bud development / mesendoderm development / negative regulation of steroid biosynthetic process / ameloblast differentiation / tricuspid valve morphogenesis / positive regulation of activin receptor signaling pathway / positive regulation of extracellular matrix constituent secretion / atrioventricular valve development / activin receptor activity / dorsal aorta morphogenesis / negative regulation of cardiac muscle cell differentiation / regulation of odontogenesis of dentin-containing tooth / endodermal-mesodermal cell signaling / corticotropin hormone secreting cell differentiation / central nervous system neuron differentiation / cardiac right ventricle morphogenesis / negative regulation of insulin-like growth factor receptor signaling pathway / thyroid-stimulating hormone-secreting cell differentiation / mesenchyme development / pharyngeal arch artery morphogenesis / aortic valve development / BMP binding / telencephalon regionalization / positive regulation of follicle-stimulating hormone secretion / hindlimb morphogenesis / cellular response to oxygen-glucose deprivation / positive regulation of phosphatase activity / positive regulation of odontogenesis / regulation of cardiac muscle cell proliferation / negative regulation of muscle cell differentiation / Sertoli cell proliferation / negative regulation of smooth muscle cell migration / positive regulation of cartilage development / proteoglycan metabolic process / heart induction / positive regulation of peroxisome proliferator activated receptor signaling pathway / sperm ejaculation / lateral mesoderm development / regulation of lateral mesodermal cell fate specification / ventricular compact myocardium morphogenesis / pericardium development / pituitary gland development / lung vasculature development / mitral valve morphogenesis / BMP receptor complex / BMP receptor activity / dorsal/ventral axis specification / embryonic skeletal system development / co-receptor binding / regulation of cellular senescence / neural crest cell development / telencephalon development / cardiac epithelial to mesenchymal transition / transforming growth factor beta receptor activity, type I / activin receptor complex / mesenchymal cell differentiation / BMP receptor binding / ectoderm development / cardiac conduction system development / positive regulation of odontoblast differentiation / endocardial cushion formation / positive regulation of bone mineralization involved in bone maturation / phosphatase activator activity / Transcriptional regulation by RUNX2 / receptor protein serine/threonine kinase / positive regulation of astrocyte differentiation / transmembrane receptor protein serine/threonine kinase activity / Signaling by BMP / activin binding / cellular response to BMP stimulus / cardiac muscle cell differentiation / activin receptor signaling pathway / outflow tract septum morphogenesis / cardiac muscle tissue morphogenesis / ventricular trabecula myocardium morphogenesis / SMAD protein signal transduction / positive regulation of ossification / astrocyte differentiation / gastrulation with mouth forming second
Similarity search - Function
: / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif ...: / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / 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. / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Cystine-knot cytokine / 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
2-acetamido-2-deoxy-alpha-D-glucopyranose / Bone morphogenetic protein 2 / Activin receptor type-2A / Bone morphogenetic protein receptor type-1A
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAllendorph, G.P. / Choe, S.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Structure of the ternary signaling complex of a TGF-beta superfamily member.
Authors: Allendorph, G.P. / Vale, W.W. / Choe, S.
History
DepositionApr 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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: Activin receptor type 2A
D: Bone morphogenetic protein 2
E: Bone morphogenetic protein receptor type IA
F: Activin receptor type 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,46010
Polymers78,5756
Non-polymers8854
Water5,891327
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.031, 104.031, 362.526
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe asymmetric unit consists of two subunits, each subunit is one half of the biological dimer. The second half of the dimer is generated by the 2-fold axis: y, x, (z-1) + 2/3

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Components

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


Mass: 12923.854 Da / Num. of mol.: 2 / Fragment: Residues 283-396
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMP2 / 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: 14344.048 Da / Num. of mol.: 2 / Fragment: Residues 24-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMPR1A / Production host: Escherichia coli (E. coli)
References: UniProt: P36894, receptor protein serine/threonine kinase
#3: Protein Activin receptor type 2A / Activin receptor type IIA / ACTR-IIA


Mass: 12019.440 Da / Num. of mol.: 2 / Fragment: Residues 20-121
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Acvr2a / Production host: Pichia pastoris (fungus)
References: UniProt: P27038, receptor protein serine/threonine kinase
#4: Sugar
ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 65.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 4M sodium formate, 100mM Hepes, 3% dioxane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.111
SYNCHROTRONSSRL BL9-221
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDAug 8, 2004
MAR3252AREA DETECTORMar 30, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 64371 / Num. obs: 62054 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.085 / Χ2: 1.062 / Net I/σ(I): 15.5
Reflection shellResolution: 2.15→2.23 Å / % possible obs: 89.4 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.402 / Num. unique obs: 5626 / Χ2: 0.989 / % possible all: 89.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.701data extraction
Blu-Icedata collection
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.259 3057 Random
Rwork0.222 --
all0.224 56988 -
obs0.224 56652 -
Displacement parametersBiso mean: 41.247 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4478 0 60 327 4865
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d1.663
LS refinement shellResolution: 2.2→2.257 Å
RfactorNum. reflection% reflection
Rfree0.308 227 -
Rwork0.249 --
obs-4012 97.54 %

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