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- PDB-9l04: Crystal structure of human ALK2 kinase domain with R206H mutation... -

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Basic information

Entry
Database: PDB / ID: 9l04
TitleCrystal structure of human ALK2 kinase domain with R206H mutation in complex with RK783
ComponentsActivin receptor type-1
KeywordsSIGNALING PROTEIN / KINASE / INHIBITOR COMPLEX
Function / homology
Function and homology information


endocardial cushion cell fate commitment / mitral valve morphogenesis / BMP receptor complex / cardiac muscle cell fate commitment / BMP receptor activity / endocardial cushion fusion / atrial septum primum morphogenesis / positive regulation of cardiac epithelial to mesenchymal transition / acute inflammatory response / positive regulation of determination of dorsal identity ...endocardial cushion cell fate commitment / mitral valve morphogenesis / BMP receptor complex / cardiac muscle cell fate commitment / BMP receptor activity / endocardial cushion fusion / atrial septum primum morphogenesis / positive regulation of cardiac epithelial to mesenchymal transition / acute inflammatory response / positive regulation of determination of dorsal identity / transforming growth factor beta receptor activity, type I / smooth muscle cell differentiation / activin receptor complex / activin receptor activity, type I / endocardial cushion formation / pharyngeal system development / transmembrane receptor protein serine/threonine kinase activity / receptor protein serine/threonine kinase / activin binding / cellular response to BMP stimulus / activin receptor signaling pathway / negative regulation of activin receptor signaling pathway / embryonic heart tube morphogenesis / gastrulation with mouth forming second / dorsal/ventral pattern formation / transforming growth factor beta binding / determination of left/right symmetry / atrioventricular valve morphogenesis / neural crest cell migration / 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 / mesoderm formation / positive regulation of intracellular signal transduction / positive regulation of SMAD protein signal transduction / regulation of ossification / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / BMP signaling pathway / 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 / apical part of cell / osteoblast differentiation / heart development / in utero embryonic development / cell differentiation / protein kinase activity / positive regulation of cell migration / cadherin binding / 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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...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 / 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
Similarity search - Domain/homology
: / Activin receptor type-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSakai, N. / Mishima-Tsumagari, C. / Shirouzu, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Bone / Year: 2025
Title: A new BMP type 1 receptor kinase inhibitor for safe and efficient oral treatment to prevent genetically induced heterotopic ossification in mice.
Authors: Yang, J. / Pan, H. / Sekimata, K. / Hwang, C. / Kulkarni, A. / Thomas, H. / Lindenau, J. / Duford, T. / Ueharu, H. / Tanaka, A. / Sakai, N. / Shirouzu, M. / Hashizume, Y. / Levi, B. / Koyama, H. / Mishina, Y.
History
DepositionDec 11, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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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)35,5918
Polymers34,5321
Non-polymers1,0597
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.037, 86.424, 140.098
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: 34531.625 Da / Num. of mol.: 1 / Mutation: R206H
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL 2 RESIDUES "SM" ARE THE RESIDUAL OF THE PURIFICATION TAG AFTER CLEAVING OFF THE TAG BY PROTEASE, FOLLOWED BY THE Q201 OF ALK2
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-A1L4C / 4-(1-ethyl-3-pyridin-3-yl-pyrazol-4-yl)-~{N}-[4-[4-(oxetan-3-yl)piperazin-1-yl]phenyl]pyrimidin-2-amine


Mass: 482.580 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H30N8O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.59 Å3/Da / Density % sol: 52.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM HEPES, 1.5 -1.6 M Ammonium sulfate / PH range: 7.6 - 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Apr 13, 2017
RadiationMonochromator: Silicon double crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→46.05 Å / Num. obs: 32655 / % possible obs: 99.46 % / Redundancy: 7.31 % / Biso Wilson estimate: 35.65 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.026 / Rrim(I) all: 0.072 / Net I/σ(I): 18.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.25-2.337.460.384.6124860.9770.1480.40898.64
2.33-2.437.430.3195.5128410.9770.1250.34399.36
2.43-2.547.470.2476.9128410.9850.0960.26599.36
2.54-2.677.410.2018.5125880.9890.0790.21699.53
2.67-2.847.430.15111126130.9940.0590.16299.24
2.84-3.067.40.10715.2128470.9960.0420.11599.71
3.06-3.367.310.07721.2125280.9960.0310.08399.65
3.36-3.857.190.05329.8124930.9980.0210.05799.71
3.85-4.857.120.04138.6126430.9990.0160.04499.78
4.85-46.056.930.03442.1127220.9990.0140.03799.51

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSVERSION Jun 30, 2024data reduction
XDSVERSION Jun 30, 2023data scaling
REFMAC5.8.0425phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JUX

6jux


Resolution: 2.25→46.04 Å / SU ML: 0.2955 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.4696
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.256 1629 4.99 %
Rwork0.195 31011 -
obs0.198 32640 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.72 Å2
Refinement stepCycle: LAST / Resolution: 2.25→46.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2351 0 66 112 2529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00872469
X-RAY DIFFRACTIONf_angle_d0.88623356
X-RAY DIFFRACTIONf_chiral_restr0.0509369
X-RAY DIFFRACTIONf_plane_restr0.0068416
X-RAY DIFFRACTIONf_dihedral_angle_d19.7993912
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.320.31091560.25982502X-RAY DIFFRACTION98.19
2.32-2.390.38821360.25012603X-RAY DIFFRACTION98.95
2.39-2.480.29681270.25072607X-RAY DIFFRACTION99.27
2.48-2.580.27581500.23282529X-RAY DIFFRACTION99.37
2.58-2.690.231580.24012564X-RAY DIFFRACTION99.52
2.69-2.840.37311230.22622594X-RAY DIFFRACTION99.52
2.84-3.010.39231400.22722597X-RAY DIFFRACTION99.74
3.01-3.250.27331370.20582603X-RAY DIFFRACTION99.75
3.25-3.570.3321040.20342616X-RAY DIFFRACTION99.71
3.57-4.090.20851370.16382591X-RAY DIFFRACTION99.78
4.09-5.150.21451370.15192606X-RAY DIFFRACTION99.75
5.15-46.040.1721240.17562599X-RAY DIFFRACTION99.71

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