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- PDB-1rew: Structural refinement of the complex of bone morphogenetic protei... -

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Basic information

Entry
Database: PDB / ID: 1rew
TitleStructural refinement of the complex of bone morphogenetic protein 2 and its type IA receptor
Components
  • bone morphogenetic protein 2
  • bone morphogenetic protein receptor type IA
KeywordsHORMONE/GROWTH FACTOR/SIGNALING PROTEIN / TGF-beta fold / BRIA-fold / 3-finger toxin fold / HORMONE-GROWTH FACTOR-SIGNALING PROTEIN COMPLEX
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 / enzyme activator complex / 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 / thyroid-stimulating hormone-secreting cell differentiation / atrioventricular valve development / cardiac right ventricle morphogenesis / positive regulation of phosphatase activity / mesenchyme development / ameloblast differentiation / aortic valve development / 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 / lung vasculature development / pericardium development / mitral valve morphogenesis / BMP receptor complex / negative regulation of smooth muscle cell migration / regulation of cellular senescence / proteoglycan metabolic process / dorsal/ventral axis specification / co-receptor binding / neural crest cell development / cardiac epithelial to mesenchymal transition / mesenchymal cell differentiation / ectoderm development / BMP receptor binding / cardiac conduction system development / telencephalon development / positive regulation of odontoblast differentiation / positive regulation of bone mineralization involved in bone maturation / endocardial cushion formation / Transcriptional regulation by RUNX2 / 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 / transmembrane receptor protein serine/threonine kinase activity / transforming growth factor beta receptor activity, type II / transforming growth factor beta receptor activity, type III / cellular response to BMP stimulus / cardiac muscle cell differentiation / Signaling by BMP / outflow tract septum morphogenesis / ventricular trabecula myocardium morphogenesis / astrocyte differentiation / positive regulation of ossification / cardiac muscle tissue morphogenesis / dorsal/ventral pattern formation / positive regulation of p38MAPK cascade / atrioventricular valve morphogenesis / positive regulation of mesenchymal cell proliferation / positive regulation of dendrite development / 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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.863 Å
AuthorsKeller, S. / Nickel, J. / Zhang, J.-L. / Sebald, W. / Mueller, T.D.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Molecular recognition of BMP-2 and BMP receptor IA.
Authors: Keller, S. / Nickel, J. / Zhang, J.L. / Sebald, W. / Mueller, T.D.
#1: Journal: Nat.Struct.Biol. / Year: 2000
Title: Crystal structure of the BMP-2-BRIA ectodomain complex
Authors: Kirsch, T. / Sebald, W. / Dreyer, M.K.
History
DepositionNov 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 2
C: bone morphogenetic protein receptor type IA
D: bone morphogenetic protein receptor type IA


Theoretical massNumber of molelcules
Total (without water)55,1974
Polymers55,1974
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-48 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.493, 107.493, 102.282
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Cell settinghexagonal
Space group name H-MP65
DetailsThe assymmetric unit contains the biological active BMP-2 dimer and two BRIA monomers

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Components

#1: Protein bone morphogenetic protein 2


Mass: 12923.854 Da / Num. of mol.: 2 / Fragment: mature part
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pN25c109 / Production host: Escherichia coli (E. coli) / References: UniProt: P12643
#2: Protein bone morphogenetic protein receptor type IA / E.C.2.7.1.37 / Serine/threonine-protein kinase receptor R5 / SKR5 / Activin receptor-like kinase 3 / ALK-3 / ...Serine/threonine-protein kinase receptor R5 / SKR5 / Activin receptor-like kinase 3 / ALK-3 / activin A receptor / type II-like kinase 3


Mass: 14674.451 Da / Num. of mol.: 2 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET32b / Production host: Escherichia coli (E. coli) / References: UniProt: P36894, EC: 2.7.1.37
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 3.88 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 7
Details: sodium acetate, imidazole, glucose, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 280K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.918 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 16, 2002
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.86→19.73 Å / Num. all: 54306 / Num. obs: 54306 / % possible obs: 96.8 % / Observed criterion σ(I): 1.2 / Redundancy: 4.6 % / Rsym value: 0.083
Reflection shellResolution: 1.86→1.91 Å / % possible all: 94.9

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Processing

Software
NameVersionClassification
REFMAC5.1refinement
SCALAdata scaling
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ES7

1es7


Resolution: 1.863→19.73 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.973 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.2 / ESU R: 0.113 / ESU R Free: 0.109 / Stereochemistry target values: REFMAC5
RfactorNum. reflection% reflectionSelection details
Rfree0.22943 2683 5 %RANDOM
Rwork0.20738 ---
obs0.2085 51294 96.46 %-
all-54306 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refine analyzeLuzzati coordinate error free: 0.109 Å
Refinement stepCycle: LAST / Resolution: 1.863→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2956 0 0 185 3141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0213047
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.9564157
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1145377
X-RAY DIFFRACTIONr_chiral_restr0.1090.2456
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022342
X-RAY DIFFRACTIONr_nbd_refined0.230.31271
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.5325
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.321
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.59
X-RAY DIFFRACTIONr_mcbond_it0.7321.51911
X-RAY DIFFRACTIONr_mcangle_it1.35523103
X-RAY DIFFRACTIONr_scbond_it2.15231136
X-RAY DIFFRACTIONr_scangle_it3.4614.51054
LS refinement shellResolution: 1.863→1.911 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 153 -
Rwork0.366 3336 -
obs-7758 94.9 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.77890.5044-0.3971.523-1.02749.3436-0.0820.2262-0.0317-0.30780.1129-0.0469-0.35840.0861-0.03090.1202-0.080.0160.11390.02830.0605-2867.23721.409
21.45070.1942-1.04970.410.069111.40030.0283-0.2003-0.0150.11750.0236-0.07610.0177-0.2629-0.0520.0524-0.05370.01140.08390.02340.0603-34.98861.42236.278
32.54231.8973-0.79879.7355-4.24045.53120.1507-0.265-0.20080.5267-0.5383-1.0099-0.45950.78070.38760.148-0.1531-0.09280.25570.08990.1204-16.88772.58145.931
47.628-2.1657-3.74133.03931.66436.7163-0.21940.41-0.61340.0940.01120.190.7256-0.57830.20820.1649-0.13270.04810.1639-0.08420.0502-41.95551.52912.367
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA12 - 11412 - 114
2X-RAY DIFFRACTION2BB12 - 11412 - 114
3X-RAY DIFFRACTION3CC32 - 11738 - 123
4X-RAY DIFFRACTION4DD32 - 12038 - 126

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