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- PDB-2k3g: NMR structure analysis of a BMP receptor -

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Basic information

Entry
Database: PDB / ID: 2k3g
TitleNMR structure analysis of a BMP receptor
ComponentsBone morphogenetic protein receptor type-1A
KeywordsSIGNALING PROTEIN / BMP / receptor / TGF-beta superfamily / ATP-binding / Disease mutation / Glycoprotein / Kinase / Magnesium / Manganese / Membrane / Metal-binding / Nucleotide-binding / Phosphoprotein / Polymorphism / Serine/threonine-protein kinase / Transferase / Transmembrane
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 / Mullerian duct regression / heart formation / atrioventricular node cell development / mesendoderm development / tricuspid valve morphogenesis ...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 / Mullerian duct regression / heart formation / atrioventricular node cell development / mesendoderm development / tricuspid valve morphogenesis / atrioventricular valve development / dorsal aorta morphogenesis / central nervous system neuron differentiation / cardiac right ventricle morphogenesis / pharyngeal arch artery morphogenesis / BMP binding / regulation of cardiac muscle cell proliferation / hindlimb morphogenesis / negative regulation of muscle cell differentiation / negative regulation of smooth muscle cell migration / lateral mesoderm development / regulation of lateral mesodermal cell fate specification / ventricular compact myocardium morphogenesis / pituitary gland development / mitral valve morphogenesis / BMP receptor activity / dorsal/ventral axis specification / regulation of cellular senescence / neural crest cell development / transforming growth factor beta receptor activity, type I / ectoderm development / cardiac conduction system development / endocardial cushion formation / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / Signaling by BMP / cellular response to BMP stimulus / outflow tract septum morphogenesis / ventricular trabecula myocardium morphogenesis / dorsal/ventral pattern formation / positive regulation of mesenchymal cell proliferation / endocardial cushion morphogenesis / embryonic digit morphogenesis / ventricular septum morphogenesis / roof of mouth development / outflow tract morphogenesis / SMAD binding / odontogenesis of dentin-containing tooth / somatic stem cell population maintenance / positive regulation of SMAD protein signal transduction / mesoderm formation / developmental growth / embryonic organ development / chondrocyte differentiation / BMP signaling pathway / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / somitogenesis / positive regulation of cardiac muscle cell proliferation / positive regulation of vascular associated smooth muscle cell proliferation / transforming growth factor beta receptor signaling pathway / epithelial cell proliferation / positive regulation of epithelial cell proliferation / lung development / HFE-transferrin receptor complex / cellular response to growth factor stimulus / positive regulation of miRNA transcription / negative regulation of neurogenesis / osteoblast differentiation / angiogenesis / in utero embryonic development / receptor complex / immune response / phosphorylation / external side of plasma membrane / negative regulation of gene expression / protein serine/threonine kinase activity / neuronal cell body / dendrite / positive regulation of gene expression / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / ATP binding / membrane / metal ion binding / plasma membrane
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 / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily ...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 / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / 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 receptor type-1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsKlages, J. / Kotzsch, A. / Mueller, T. / Kessler, H.
CitationJournal: Biochemistry / Year: 2008
Title: The solution structure of BMPR-IA reveals a local disorder-to-order transition upon BMP-2 binding.
Authors: Klages, J. / Kotzsch, A. / Coles, M. / Sebald, W. / Nickel, J. / Muller, T. / Kessler, H.
History
DepositionMay 7, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bone morphogenetic protein receptor type-1A


Theoretical massNumber of molelcules
Total (without water)11,2791
Polymers11,2791
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 50structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Bone morphogenetic protein receptor type-1A / Serine/threonine-protein kinase receptor R5 / SKR5 / Activin receptor-like kinase 3 / ALK-3 / CD292 antigen


Mass: 11278.693 Da / Num. of mol.: 1 / Fragment: Extracellular domain (UNP residues 51-152) / Mutation: A28G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMPR1A, ACVRLK3, ALK3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P36894, receptor protein serine/threonine kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1222D 1H-13C HSQC
1323D HNCO
1423D HNCA
1523D CBCA(CO)NH
1623D HBHA(CO)NH
1723D HN(CA)CB
1823D C(CO)NH
1923D (H)CCH-TOCSY
11013D HNHA
11122D 1H-1H NOESY
11223D 1H-15N NOESY
11323D 1H-13C NOESY
11413D HNHB
11523D (H)CCH-COSY
11623D 1H-15N-15N NOESY
11723D 1H-15N-13C NIOESY
11823D (H)CCH-TOCSY
11923D HN(CA)HA
12023D HN(CA)CO

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Sample preparation

Details
Solution-IDContentsSolvent system
11.1 mM [U-99% 15N] Bone Morphogenetic Protein Receptor Type IA, 10 mM potassium phosphate, 0.2 w/v sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
20.5 mM [U-94% 13C; U-98% 15N] Bone Morphogenetic Protein Receptor Type IA, 10 mM potassium phosphate, 0.2 w/v sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMBone Morphogenetic Protein Receptor Type IA[U-99% 15N]1
95 v/vH2O1
5 v/vD2O1
10 mMpotassium phosphate1
0.2 w/vsodium azide1
0.5 mMBone Morphogenetic Protein Receptor Type IA[U-94% 13C; U-98% 15N]2
95 v/vH2O2
5 v/vD2O2
10 mMpotassium phosphate2
0.2 w/vsodium azide2
Sample conditionspH: 6.3 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker DMXBrukerDMX7502
Bruker DMXBrukerDMX6003
Bruker DMXBrukerDMX6004

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.9.4aSchwieters, Kuszewski, Tjandra and Clorestructure solution
TopSpin1.3Bruker Biospinprocessing
TopSpin1.3Bruker Biospincollection
SparkyGoddarddata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
ProcheckNMRLaskowski and MacArthurgeometry optimization
AQUARullmann, Doreleijers and Kapteingeometry optimization
WHAT IFVriendgeometry optimization
X-PLOR NIH2.9.4aSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: standard protocols were used
NMR constraintsNOE constraints total: 699 / NOE intraresidue total count: 167 / NOE long range total count: 182 / NOE medium range total count: 57 / NOE sequential total count: 249
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 21
NMR ensemble rmsDistance rms dev: 0.022 Å / Distance rms dev error: 0.002 Å

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