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- PDB-2lcr: NMR Structure of Alk1 extracellular domain -

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Basic information

Entry
Database: PDB / ID: 2lcr
TitleNMR Structure of Alk1 extracellular domain
ComponentsActivin receptor-like kinase 1
KeywordsTRANSFERASE
Function / homology
Function and homology information


lymphatic endothelial cell differentiation / regulation of endothelial cell proliferation / negative regulation of endothelial cell differentiation / dorsal aorta morphogenesis / positive regulation of epithelial cell differentiation / blood vessel maturation / lymphangiogenesis / venous blood vessel development / transforming growth factor beta receptor activity / retina vasculature development in camera-type eye ...lymphatic endothelial cell differentiation / regulation of endothelial cell proliferation / negative regulation of endothelial cell differentiation / dorsal aorta morphogenesis / positive regulation of epithelial cell differentiation / blood vessel maturation / lymphangiogenesis / venous blood vessel development / transforming growth factor beta receptor activity / retina vasculature development in camera-type eye / positive regulation of chondrocyte differentiation / BMP receptor complex / BMP receptor activity / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of endothelial cell differentiation / activin receptor activity, type I / transforming growth factor beta receptor activity, type I / negative regulation of focal adhesion assembly / endothelial tube morphogenesis / positive regulation of bicellular tight junction assembly / regulation of blood vessel endothelial cell migration / artery development / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / Signaling by BMP / activin binding / cellular response to BMP stimulus / positive regulation of BMP signaling pathway / negative regulation of cell adhesion / transforming growth factor beta binding / dorsal/ventral pattern formation / blood circulation / wound healing, spreading of epidermal cells / negative regulation of endothelial cell migration / endocardial cushion morphogenesis / positive regulation of Notch signaling pathway / SMAD binding / negative regulation of endothelial cell proliferation / regulation of DNA replication / positive regulation of SMAD protein signal transduction / negative regulation of blood vessel endothelial cell migration / blood vessel remodeling / BMP signaling pathway / cellular response to transforming growth factor beta stimulus / positive regulation of endothelial cell proliferation / transforming growth factor beta receptor signaling pathway / negative regulation of cell migration / negative regulation of cell growth / cellular response to growth factor stimulus / regulation of blood pressure / positive regulation of angiogenesis / heart development / angiogenesis / in utero embryonic development / response to hypoxia / negative regulation of cell population proliferation / phosphorylation / negative regulation of gene expression / protein serine/threonine kinase activity / neuronal cell body / dendrite / regulation of DNA-templated transcription / protein kinase binding / positive regulation of DNA-templated transcription / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Ribbon / Protein tyrosine and serine/threonine kinase ...GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Ribbon / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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
Serine/threonine-protein kinase receptor R3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsIlangovan, U.
CitationJournal: Biochemistry / Year: 2012
Title: Structure of the Alk1 extracellular domain and characterization of its bone morphogenetic protein (BMP) binding properties.
Authors: Mahlawat, P. / Ilangovan, U. / Biswas, T. / Sun, L.Z. / Hinck, A.P.
History
DepositionMay 6, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Activin receptor-like kinase 1


Theoretical massNumber of molelcules
Total (without water)11,1491
Polymers11,1491
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 200structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Activin receptor-like kinase 1 / Serine/threonine-protein kinase receptor R3 / SKR3 / ALK-1 / TGF-B superfamily receptor type I / TSR-I


Mass: 11148.556 Da / Num. of mol.: 1 / Fragment: Extracellular domain residues 22-118
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACVRL1, ACVRLK1, ALK1 / Production host: Escherichia coli (E. coli)
References: UniProt: P37023, 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
1112D 1H-15N HSQC
1222D 1H-13C HSQC aliphatic
1323D HN(CA)CB
1423D CBCA(CO)NH
1523D HNCA
1623D C(CO)NH
1723D HBHA(CO)NH
1823D HNCO
1913D HNHA
11023D (H)CCH-TOCSY
11113D 1H-15N NOESY
11223D 1H-13C NOESY
11332D 15N-HSQC IPAP

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 15N] Alk1, 25 mM sodium phosphate, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
20.5 mM [U-100% 13C; U-100% 15N] Alk1, 25 mM sodium phosphate, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
30.5 mM [U-100% 13C; U-100% 15N] Alk1, 25 mM sodium phosphate, 0.02 % sodium azide, 5mg/mL mg Pf1 phage, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMAlk1-1[U-100% 15N]1
25 mMsodium phosphate-21
0.02 %sodium azide-31
0.5 mMAlk1-4[U-100% 13C; U-100% 15N]2
25 mMsodium phosphate-52
0.02 %sodium azide-62
0.5 mMAlk1-7[U-100% 13C; U-100% 15N]3
25 mMsodium phosphate-83
0.02 %sodium azide-93
5 mg/mLPf1 phage-103
Sample conditionspH: 5.5 / Pressure: ambient / Temperature: 305 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue and Nilgesstructure solution
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
ModelFreePalmerrealaxation
MOLMOLKoradi, Billeter and Wuthrichstructure visualization
PECANEghbalnia, Wang, Bahrami, Assadi, and Markleychemical shift index calculation
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxspectral visualization
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata processing
SparkyGoddardchemical shift assignment
TALOSCornilescu, Delaglio and Baxdihedral angle determination
TopSpinBruker Biospindata collection
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1612 / Disulfide bond constraints total count: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 15

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