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- PDB-2qj9: Crystal structure analysis of BMP-2 in complex with BMPR-IA variant B1 -

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Basic information

Entry
Database: PDB / ID: 2qj9
TitleCrystal structure analysis of BMP-2 in complex with BMPR-IA variant B1
Components
  • Bone morphogenetic protein 2
  • Bone morphogenetic protein receptor type IA
KeywordsCytokine/Receptor / ligand-receptor complex / Chondrogenesis / Cleavage on pair of basic residues / Cytokine / Developmental protein / Differentiation / Glycoprotein / Growth factor / Osteogenesis / ATP-binding / Disease mutation / Kinase / Magnesium / Manganese / Membrane / Metal-binding / Nucleotide-binding / Phosphorylation / Serine/threonine-protein kinase / Transferase / Transmembrane / Cytokine-Receptor 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: 2.44 Å
AuthorsKotzsch, A. / Mueller, T.D.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structure analysis of bone morphogenetic protein-2 type I receptor complexes reveals a mechanism of receptor inactivation in juvenile polyposis syndrome.
Authors: Kotzsch, A. / Nickel, J. / Seher, A. / Heinecke, K. / van Geersdaele, L. / Herrmann, T. / Sebald, W. / Mueller, T.D.
History
DepositionJul 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 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 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 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
B: Bone morphogenetic protein 2
A: Bone morphogenetic protein 2
D: Bone morphogenetic protein receptor type IA
C: Bone morphogenetic protein receptor type IA


Theoretical massNumber of molelcules
Total (without water)55,7274
Polymers55,7274
Non-polymers00
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7172 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.961, 105.961, 96.789
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 13126.128 Da / Num. of mol.: 2 / Fragment: mature part (residues 283-396)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMP2, BMP2A / Plasmid: pET32a / 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: 14737.469 Da / Num. of mol.: 2 / Fragment: extracellular domain (residues 24-152) / Mutation: K88R,S90T,K92I,A93P,Q94H,L95Q,T98S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMPR1A, ACVRLK3, ALK3 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / References: UniProt: P36894
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.88 Å3/Da / Density % sol: 57.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.8M K Na phosphate, 25% ethylene glycol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9796 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 25, 2005
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.44→34.68 Å / Num. all: 22783 / Num. obs: 22783 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.11 % / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 13.8
Reflection shellResolution: 2.44→2.53 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.339 / % possible all: 93.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1REW

1rew


Resolution: 2.44→30.59 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.926 / SU B: 12.303 / SU ML: 0.148 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.296 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25338 1160 5.1 %RANDOM
Rwork0.19706 ---
obs0.19976 21585 99.05 %-
all-23743 --
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: 87.859 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.243 Å0.296 Å
Refinement stepCycle: LAST / Resolution: 2.44→30.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3008 0 0 182 3190
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223106
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.9524245
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4575382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59724.861144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.06815482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8581512
X-RAY DIFFRACTIONr_chiral_restr0.1040.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022410
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.250.31448
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3280.52130
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2180.5334
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2880.347
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3520.510
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8351.51969
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.50323157
X-RAY DIFFRACTIONr_scbond_it1.81631261
X-RAY DIFFRACTIONr_scangle_it2.7834.51088
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.44→2.506 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 84 -
Rwork0.326 1451 -
obs--90.83 %
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)
11.3850.6216-0.86911.7758-1.53910.5350.10540.0028-0.1878-0.07410.0707-0.1448-0.4447-0.0665-0.1761-0.2234-0.13780.0144-0.30430.0424-0.133827.6914-23.5932-5.3071
22.12490.6513-1.44911.2672-0.069910.06520.2659-0.6631-0.17010.3512-0.0243-0.2139-0.2719-0.0705-0.2416-0.2462-0.127-0.0584-0.10370.1125-0.141921.1035-29.76489.3477
35.05510.7065-0.824410.435-4.87778.28190.2627-0.7729-0.45891.3847-0.4174-1.1497-0.28740.15930.15470.0534-0.2657-0.304-0.11920.0978-0.085739.1175-17.281518.7973
47.9195-1.81-3.62362.82031.60645.7618-0.08820.3829-0.6007-0.0751-0.02090.04750.1067-0.15980.1091-0.3596-0.08880.0247-0.2151-0.0689-0.177815.745-40.429-15.3856
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AB12 - 9214 - 94
2X-RAY DIFFRACTION1AB96 - 11498 - 116
3X-RAY DIFFRACTION2BA12 - 9214 - 94
4X-RAY DIFFRACTION2BA96 - 11498 - 116
5X-RAY DIFFRACTION3CD32 - 8838 - 94
6X-RAY DIFFRACTION3CD96 - 116102 - 122
7X-RAY DIFFRACTION4DC32 - 12138 - 127

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