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- PDB-2qjb: Crystal structure analysis of BMP-2 in complex with BMPR-IA varia... -

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Basic information

Entry
Database: PDB / ID: 2qjb
TitleCrystal structure analysis of BMP-2 in complex with BMPR-IA variant IA/IB
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 / cardiac atrium formation / positive regulation of transforming growth factor beta2 production / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / positive regulation of phosphatase activity / cardiac jelly development ...neural plate mediolateral regionalization / paraxial mesoderm structural organization / positive regulation of cardiac ventricle development / fibrous ring of heart morphogenesis / cardiac atrium formation / positive regulation of transforming growth factor beta2 production / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / positive regulation of phosphatase activity / cardiac jelly development / Mullerian duct regression / positive regulation of extracellular matrix constituent secretion / negative regulation of aldosterone biosynthetic process / heart formation / negative regulation of cortisol biosynthetic process / atrioventricular node cell development / atrioventricular canal morphogenesis / negative regulation of steroid biosynthetic process / embryonic heart tube anterior/posterior pattern specification / mesenchymal cell proliferation involved in ureteric bud development / mesendoderm development / enzyme activator complex / regulation of odontogenesis of dentin-containing tooth / dorsal aorta morphogenesis / endodermal-mesodermal cell signaling / tricuspid valve morphogenesis / negative regulation of cardiac muscle cell differentiation / corticotropin hormone secreting cell differentiation / thyroid-stimulating hormone-secreting cell differentiation / mesenchyme development / cardiac right ventricle morphogenesis / atrioventricular valve development / negative regulation of insulin-like growth factor receptor signaling pathway / ameloblast differentiation / aortic valve development / pericardium development / telencephalon regionalization / BMP binding / hindlimb morphogenesis / regulation of cardiac muscle cell proliferation / negative regulation of muscle cell differentiation / pharyngeal arch artery morphogenesis / heart induction / positive regulation of cartilage development / positive regulation of odontogenesis / regulation of lateral mesodermal cell fate specification / positive regulation of peroxisome proliferator activated receptor signaling pathway / lateral mesoderm development / pituitary gland development / mitral valve morphogenesis / BMP receptor complex / negative regulation of smooth muscle cell migration / BMP receptor activity / regulation of cellular senescence / proteoglycan metabolic process / ventricular compact myocardium morphogenesis / dorsal/ventral axis specification / co-receptor binding / lung vasculature development / neural crest cell development / cardiac epithelial to mesenchymal transition / mesenchymal cell differentiation / transforming growth factor beta receptor activity, type I / ectoderm development / telencephalon development / BMP receptor binding / positive regulation of bone mineralization involved in bone maturation / positive regulation of odontoblast differentiation / cardiac conduction system development / phosphatase activator activity / Transcriptional regulation by RUNX2 / endocardial cushion formation / positive regulation of astrocyte differentiation / transmembrane receptor protein serine/threonine kinase activity / receptor protein serine/threonine kinase / cellular response to BMP stimulus / Signaling by BMP / cardiac muscle cell differentiation / ventricular trabecula myocardium morphogenesis / astrocyte differentiation / outflow tract septum morphogenesis / cardiac muscle tissue morphogenesis / positive regulation of ossification / dorsal/ventral pattern formation / positive regulation of p38MAPK cascade / central nervous system neuron differentiation / atrioventricular valve morphogenesis / positive regulation of dendrite development / positive regulation of mesenchymal cell proliferation / endocardial cushion morphogenesis / Molecules associated with elastic fibres / embryonic digit morphogenesis / branching involved in ureteric bud morphogenesis / positive regulation of osteoblast proliferation / ventricular septum morphogenesis / negative regulation of fat cell differentiation / SMAD binding / bone mineralization / odontogenesis of dentin-containing tooth / negative regulation of cell cycle
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 / Transforming growth factor beta, conserved site / Activin types I and II receptor domain ...: / 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 / Transforming growth factor beta, conserved site / Activin types I and II receptor domain / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.4Nov 13, 2024Group: Structure summary / Category: 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 2
C: Bone morphogenetic protein receptor type IA
D: Bone morphogenetic protein receptor type IA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8295
Polymers55,7934
Non-polymers351
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7229 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.175, 104.175, 100.012
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: 14770.498 Da / Num. of mol.: 2 / Fragment: extracellular domain (residues 24-152)
Mutation: K88R,S90T,K92I,A93P,Q94H,L95Q,T98S,A74T,M78L,K79G,Y80L,D46E,G42H,A61T,I62M
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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 57.26 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 4, 2005
RadiationMonochromator: Varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→31.27 Å / Num. all: 21360 / Num. obs: 21360 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.23 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 11.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.32 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.564 / % possible all: 99.9

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Processing

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

1rew


Resolution: 2.5→31.27 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.917 / SU B: 13.961 / SU ML: 0.152 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.32 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26259 1097 5.1 %RANDOM
Rwork0.20388 ---
obs0.20682 20259 99.79 %-
all-21290 --
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: 81.516 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å2-0.55 Å20 Å2
2---1.1 Å20 Å2
3---1.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.5→31.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2972 0 1 79 3052
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213067
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.9514195
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7725378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.7224.93142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.57715478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4821512
X-RAY DIFFRACTIONr_chiral_restr0.0990.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022368
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2750.31435
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3340.52099
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.5208
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3450.333
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3960.53
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7291.51951
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.33823126
X-RAY DIFFRACTIONr_scbond_it1.63431234
X-RAY DIFFRACTIONr_scangle_it2.54.51069
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 79 -
Rwork0.313 1496 -
obs--99.81 %
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)
12.44260.21811.23861.1993-0.37698.6375-0.006-0.08720.22990.1244-0.0878-0.12370.07610.36170.0937-0.4398-0.05240.0044-0.1681-0.0064-0.168745.4132-54.3152-23.266
22.04450.41110.8161.94990.38487.8771-0.04880.42410.3019-0.2660.1719-0.14020.23070.2204-0.1231-0.3829-0.06680.0162-0.1775-0.0014-0.192436.4553-56.98-36.6947
39.2046-1.93612.95336.4524-0.13687.0362-0.33271.49261.0843-0.33420.230.195-0.50670.04830.1028-0.3194-0.10590.05570.28490.2624-0.068756.692-47.5659-46.4241
42.939-0.01260.34678.45332.83476.36390.0798-0.10740.31140.3120.03460.3527-0.1902-0.2032-0.1144-0.2704-0.11530.1047-0.2346-0.055-0.174824.4883-56.8206-12.6529
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA12 - 9214 - 94
2X-RAY DIFFRACTION1AA98 - 114100 - 116
3X-RAY DIFFRACTION2BB12 - 9214 - 94
4X-RAY DIFFRACTION2BB98 - 114100 - 116
5X-RAY DIFFRACTION3CC32 - 8838 - 94
6X-RAY DIFFRACTION3CC96 - 116102 - 122
7X-RAY DIFFRACTION4DD32 - 12138 - 127

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