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- PDB-6unr: Kinase domain of ALK2-K492A/K493A with AMPPNP -

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Basic information

Entry
Database: PDB / ID: 6unr
TitleKinase domain of ALK2-K492A/K493A with AMPPNP
ComponentsActivin receptor type-1
KeywordsTRANSFERASE / Kinase
Function / homology
Function and homology information


endocardial cushion cell fate commitment / mitral valve morphogenesis / endocardial cushion fusion / BMP receptor complex / atrial septum primum morphogenesis / BMP receptor activity / cardiac muscle cell fate commitment / acute inflammatory response / activin receptor activity, type I / positive regulation of cardiac epithelial to mesenchymal transition ...endocardial cushion cell fate commitment / mitral valve morphogenesis / endocardial cushion fusion / BMP receptor complex / atrial septum primum morphogenesis / BMP receptor activity / cardiac muscle cell fate commitment / acute inflammatory response / activin receptor activity, type I / positive regulation of cardiac epithelial to mesenchymal transition / positive regulation of determination of dorsal identity / transforming growth factor beta receptor activity, type I / activin receptor complex / endocardial cushion formation / smooth muscle cell differentiation / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / pharyngeal system development / activin binding / cellular response to BMP stimulus / activin receptor signaling pathway / negative regulation of activin receptor signaling pathway / transforming growth factor beta binding / embryonic heart tube morphogenesis / gastrulation with mouth forming second / dorsal/ventral pattern formation / determination of left/right symmetry / neural crest cell migration / atrioventricular valve morphogenesis / branching involved in blood vessel morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / ventricular septum morphogenesis / SMAD binding / germ cell development / peptide hormone binding / positive regulation of SMAD protein signal transduction / mesoderm formation / regulation of ossification / BMP signaling pathway / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / negative regulation of signal transduction / transforming growth factor beta receptor signaling pathway / protein tyrosine kinase binding / negative regulation of extrinsic apoptotic signaling pathway / cellular response to growth factor stimulus / positive regulation of peptidyl-tyrosine phosphorylation / apical part of cell / heart development / in utero embryonic development / protein kinase activity / positive regulation of cell migration / cadherin binding / phosphorylation / protein serine/threonine kinase activity / positive regulation of DNA-templated transcription / protein homodimerization activity / 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 / Activin types I and II receptor domain / Activin types I and II receptor domain / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain ...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 / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / 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. / 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
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Activin receptor type-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAgnew, C. / Jura, N.
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis for ALK2/BMPR2 receptor complex signaling through kinase domain oligomerization.
Authors: Agnew, C. / Ayaz, P. / Kashima, R. / Loving, H.S. / Ghatpande, P. / Kung, J.E. / Underbakke, E.S. / Shan, Y. / Shaw, D.E. / Hata, A. / Jura, N.
History
DepositionOct 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Activin receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,76010
Polymers38,0591
Non-polymers7019
Water21612
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, ALK2-K492A/K493A mutant kinase domain is a monomer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.122, 87.124, 138.916
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Activin receptor type-1 / Activin receptor type I / ACTR-I / Activin receptor-like kinase 2 / ALK-2 / Serine/threonine- ...Activin receptor type I / ACTR-I / Activin receptor-like kinase 2 / ALK-2 / Serine/threonine-protein kinase receptor R1 / SKR1 / TGF-B superfamily receptor type I / TSR-I


Mass: 38059.336 Da / Num. of mol.: 1 / Fragment: Kinase domain / Mutation: K492A, K493A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACVR1, ACVRLK2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q04771, receptor protein serine/threonine kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.35 Å3/Da / Density % sol: 47.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.05 M PIPES 7 pH, 0.01 M DTT, 10 %w/v PEG 4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1111 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1111 Å / Relative weight: 1
ReflectionResolution: 2.2→48.92 Å / Num. obs: 18605 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 42.4 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.06 / Rrim(I) all: 0.119 / Net I/σ(I): 10.6
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 1.172 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1571 / CC1/2: 0.929 / Rpim(I) all: 0.685 / Rrim(I) all: 1.361

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q4U

3q4u


Resolution: 2.2→46.14 Å / SU ML: 0.3484 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.7216
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3025 889 4.81 %
Rwork0.2435 17576 -
obs0.2461 18465 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.05 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2185 0 39 12 2236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00342265
X-RAY DIFFRACTIONf_angle_d0.74283095
X-RAY DIFFRACTIONf_chiral_restr0.0448362
X-RAY DIFFRACTIONf_plane_restr0.0043386
X-RAY DIFFRACTIONf_dihedral_angle_d11.33431330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.340.45411640.40692817X-RAY DIFFRACTION98.64
2.34-2.520.45781490.34732889X-RAY DIFFRACTION98.76
2.52-2.770.36071400.30172908X-RAY DIFFRACTION99.15
2.77-3.170.32181380.28562912X-RAY DIFFRACTION99.32
3.17-40.30191610.23022948X-RAY DIFFRACTION99.74
4-46.140.23041370.19123102X-RAY DIFFRACTION99.85
Refinement TLS params.Method: refined / Origin x: 13.5349426149 Å / Origin y: 18.5918193248 Å / Origin z: -17.416687112 Å
111213212223313233
T0.446501562113 Å20.127050057065 Å2-0.0355348066713 Å2-0.51694616261 Å2-0.0440196340444 Å2--0.380823702461 Å2
L3.71419724247 °20.616777558724 °20.303950399956 °2-1.40760365432 °2-0.164378070671 °2--9.2794074884 °2
S0.139788002537 Å °-0.0425723051817 Å °-0.0490783476532 Å °0.146363321624 Å °0.0903155012377 Å °0.00223186292311 Å °-0.0292530479254 Å °-0.891879703425 Å °-0.181694572238 Å °
Refinement TLS groupSelection details: all

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