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- PDB-6t8n: Crystal structure of the ACVR1 (ALK2) kinase in complex with the ... -

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Basic information

Entry
Database: PDB / ID: 6t8n
TitleCrystal structure of the ACVR1 (ALK2) kinase in complex with the compound M4K3007
ComponentsActivin receptor type I
KeywordsSIGNALING PROTEIN / KINASE / BMP / INHIBITOR / SIGNALLING
Function / homology
Function and homology information


endocardial cushion cell fate commitment / mitral valve morphogenesis / BMP receptor complex / endocardial cushion fusion / 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 / BMP receptor complex / endocardial cushion fusion / 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 / activin receptor complex / transforming growth factor beta receptor activity, type I / positive regulation of determination of dorsal identity / 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 / embryonic heart tube morphogenesis / transforming growth factor beta binding / gastrulation with mouth forming second / dorsal/ventral pattern formation / determination of left/right symmetry / neural crest cell migration / atrioventricular valve morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / ventricular septum morphogenesis / branching involved in blood vessel morphogenesis / SMAD binding / germ cell development / positive regulation of SMAD protein signal transduction / peptide hormone binding / mesoderm formation / regulation of ossification / BMP signaling pathway / positive regulation of osteoblast differentiation / positive regulation of bone mineralization / negative regulation of signal transduction / protein tyrosine kinase binding / transforming growth factor beta receptor signaling pathway / 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 / 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 / Transferase(Phosphotransferase) 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 / Protein tyrosine and serine/threonine kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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
Chem-MVE / L(+)-TARTARIC ACID / Activin receptor type-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsAdamson, R.J. / Williams, E.P. / Bonomo, S. / Rankin, S. / Bacos, D. / Rae, A. / Cramp, S. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. ...Adamson, R.J. / Williams, E.P. / Bonomo, S. / Rankin, S. / Bacos, D. / Rae, A. / Cramp, S. / 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 M4K3007
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
DepositionOct 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2019Provider: 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)70,86112
Polymers69,0752
Non-polymers1,78610
Water2,828157
1
A: Activin receptor type I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3635
Polymers34,5381
Non-polymers8254
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Activin receptor type I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4997
Polymers34,5381
Non-polymers9616
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.270, 69.230, 164.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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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: Sequence contains a deliberate mutation at Q207D. / 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, 167 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical ChemComp-MVE / cyclopropyl-[4-[6-[5-(4-ethoxy-1-propan-2-yl-piperidin-4-yl)pyridin-2-yl]pyrrolo[1,2-b]pyridazin-4-yl]piperazin-1-yl]methanone


Mass: 516.678 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H40N6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.19 Å3/Da / Density % sol: 43.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M citrate pH 5.5 1.2M ammonium sulfate 0.4M sodium/potassium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 21, 2019 / Details: Compound Refractive Lenses
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.77→82.35 Å / Num. obs: 59021 / % possible obs: 99.6 % / Redundancy: 13 % / Biso Wilson estimate: 26.51 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.204 / Rpim(I) all: 0.059 / Rrim(I) all: 0.213 / Χ2: 1.01 / Net I/σ(I): 8.9
Reflection shellResolution: 1.77→1.82 Å / Redundancy: 12.2 % / Rmerge(I) obs: 2.545 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4289 / CC1/2: 0.518 / Rpim(I) all: 0.757 / Rrim(I) all: 2.658 / Χ2: 0.84 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
xia20.5.771data reduction
Aimless0.7.3data scaling
PHASER2.8.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SRH

6srh


Resolution: 1.77→82.34 Å / SU ML: 0.2495 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.8599
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2884 4.89 %Random selection
Rwork0.203 ---
obs0.2046 58923 99.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.01 Å2
Refinement stepCycle: LAST / Resolution: 1.77→82.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4668 0 118 157 4943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01034947
X-RAY DIFFRACTIONf_angle_d1.21016730
X-RAY DIFFRACTIONf_chiral_restr0.0674744
X-RAY DIFFRACTIONf_plane_restr0.0069832
X-RAY DIFFRACTIONf_dihedral_angle_d11.4522907
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.80.34321540.34442608X-RAY DIFFRACTION99.71
1.8-1.830.36531520.33922598X-RAY DIFFRACTION99.71
1.83-1.860.32841260.30262665X-RAY DIFFRACTION99.57
1.86-1.90.35041460.29362597X-RAY DIFFRACTION99.53
1.9-1.940.35641560.32342637X-RAY DIFFRACTION99.68
1.94-1.980.28561100.2582661X-RAY DIFFRACTION99.64
1.98-2.030.30491320.25042630X-RAY DIFFRACTION99.17
2.03-2.080.29581410.24212617X-RAY DIFFRACTION99.53
2.08-2.130.29931290.24032637X-RAY DIFFRACTION99.18
2.13-2.20.30471160.2372673X-RAY DIFFRACTION99.75
2.2-2.270.32021370.26032649X-RAY DIFFRACTION99.57
2.27-2.350.2631480.21742652X-RAY DIFFRACTION99.54
2.35-2.440.20871460.1962626X-RAY DIFFRACTION99.57
2.44-2.550.23681350.19642678X-RAY DIFFRACTION99.26
2.55-2.690.2311260.192662X-RAY DIFFRACTION99.71
2.69-2.860.23161320.19672675X-RAY DIFFRACTION99.5
2.86-3.080.26091300.2042728X-RAY DIFFRACTION99.86
3.08-3.390.23611320.22687X-RAY DIFFRACTION99.47
3.39-3.880.22451530.17682712X-RAY DIFFRACTION99.79
3.88-4.880.15941460.1352758X-RAY DIFFRACTION99.73
4.88-82.340.1791370.18762889X-RAY DIFFRACTION98.92

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