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- PDB-6z36: Crystal structure of the ACVR1 (ALK2) kinase in complex with the ... -

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Basic information

Entry
Database: PDB / ID: 6z36
TitleCrystal structure of the ACVR1 (ALK2) kinase in complex with the compound M4K2118
ComponentsActivin receptor type I
KeywordsSIGNALING PROTEIN / Kinase / inhibitor complex / receptor
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 / atrial septum primum morphogenesis / endocardial cushion fusion / 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 / atrial septum primum morphogenesis / endocardial cushion fusion / 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 / ventricular septum morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / SMAD binding / germ cell development / peptide hormone binding / positive regulation of intracellular signal transduction / mesoderm formation / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
AMMONIUM ION / Chem-Q5Z / D(-)-TARTARIC ACID / Activin receptor type-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsAdamson, R.J. / Williams, E.P. / Smil, D. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.N.
CitationJournal: To Be Published
Title: Crystal structure of the ACVR1 (ALK2) kinase in complex with the compound M4K2118
Authors: Adamson, R.J. / Williams, E.P. / Smil, D. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.N.
History
DepositionMay 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Activin receptor type I
B: Activin receptor type I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,71417
Polymers69,0752
Non-polymers2,63915
Water10,683593
1
A: Activin receptor type I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2949
Polymers34,5381
Non-polymers1,7568
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Activin receptor type I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4218
Polymers34,5381
Non-polymers8837
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.434, 84.607, 88.378
Angle α, β, γ (deg.)90.000, 131.007, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Activin receptor type I


Mass: 34537.633 Da / Num. of mol.: 2 / Mutation: Q207D
Source method: isolated from a genetically manipulated source
Details: Contains a Q207D mutation compared to the published sequence.
Source: (gene. exp.) Homo sapiens (human) / Gene: ACVR1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q04771, receptor protein serine/threonine kinase

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Non-polymers , 6 types, 608 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical
ChemComp-Q5Z / 4-methyl-3-(4-piperidin-4-ylphenyl)-5-(3,4,5-trimethoxyphenyl)pyridine


Mass: 418.528 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H30N2O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 593 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 0.1M Citrate pH 5.2, 1.2M ammonium sulphate, 0.2M sodiuim/potassium tartarate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 100K-M / Detector: PIXEL / Date: Jan 21, 2019
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.37→66.69 Å / Num. obs: 128068 / % possible obs: 99.8 % / Redundancy: 13.1 % / Biso Wilson estimate: 13.99 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.229 / Rpim(I) all: 0.066 / Rrim(I) all: 0.239 / Χ2: 0.96 / Net I/σ(I): 8.3
Reflection shellResolution: 1.37→1.52 Å / Redundancy: 13.3 % / Rmerge(I) obs: 6.02 / Mean I/σ(I) obs: 1 / Num. unique obs: 18629 / CC1/2: 0.473 / Rpim(I) all: 1.72 / Rrim(I) all: 6.266 / Χ2: 0.91 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDS1.0.5data reduction
Aimless0.7.3data scaling
PHASER2.8.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6srh

6srh


Resolution: 1.37→66.69 Å / SU ML: 0.1332 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1465
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1905 5616 5.09 %
Rwork0.1487 104766 -
obs0.1509 110382 74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.56 Å2
Refinement stepCycle: LAST / Resolution: 1.37→66.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4590 0 178 593 5361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00965000
X-RAY DIFFRACTIONf_angle_d1.03376811
X-RAY DIFFRACTIONf_chiral_restr0.0766741
X-RAY DIFFRACTIONf_plane_restr0.0061850
X-RAY DIFFRACTIONf_dihedral_angle_d22.4894710
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.380.14770.1903112X-RAY DIFFRACTION2.43
1.38-1.40.3561110.2051366X-RAY DIFFRACTION7.67
1.4-1.420.2168360.2327720X-RAY DIFFRACTION15.25
1.42-1.430.265470.21551063X-RAY DIFFRACTION22.64
1.43-1.450.2529680.21661343X-RAY DIFFRACTION28.45
1.45-1.470.2781880.20551712X-RAY DIFFRACTION36.05
1.47-1.490.2491860.22091X-RAY DIFFRACTION43.76
1.49-1.520.27271370.1992323X-RAY DIFFRACTION50.43
1.52-1.540.28271660.18872597X-RAY DIFFRACTION55.66
1.54-1.560.27931730.18992936X-RAY DIFFRACTION62.34
1.56-1.590.22121770.19553227X-RAY DIFFRACTION68.44
1.59-1.620.21161760.1863458X-RAY DIFFRACTION73.55
1.62-1.650.22292000.18543728X-RAY DIFFRACTION79.19
1.65-1.690.23552030.17734042X-RAY DIFFRACTION85.21
1.69-1.720.23322600.18164286X-RAY DIFFRACTION91.47
1.72-1.760.22222390.17284559X-RAY DIFFRACTION97.34
1.76-1.810.21422390.16364715X-RAY DIFFRACTION99.86
1.81-1.860.21982510.15994712X-RAY DIFFRACTION99.94
1.86-1.910.20212500.14854727X-RAY DIFFRACTION99.84
1.91-1.970.18762490.14494720X-RAY DIFFRACTION99.5
1.97-2.040.16372350.12894698X-RAY DIFFRACTION100
2.04-2.120.18232470.12684749X-RAY DIFFRACTION99.92
2.12-2.220.17142250.12434714X-RAY DIFFRACTION100
2.22-2.340.16732660.1274736X-RAY DIFFRACTION99.86
2.34-2.480.17612390.1324744X-RAY DIFFRACTION100
2.48-2.680.18152830.14444693X-RAY DIFFRACTION100
2.68-2.940.19722610.15454747X-RAY DIFFRACTION100
2.95-3.370.18572840.14994709X-RAY DIFFRACTION99.98
3.37-4.250.17012700.13144765X-RAY DIFFRACTION100
4.25-66.690.17942430.15474774X-RAY DIFFRACTION98.45

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