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- PDB-7a21: Crystal structure of the ACVR1 (ALK2) kinase in complex with the ... -

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Basic information

Entry
Database: PDB / ID: 7a21
TitleCrystal structure of the ACVR1 (ALK2) kinase in complex with the compound M4K2158
ComponentsActivin receptor type I
KeywordsSIGNALING PROTEIN / Kinase / inhibitor complex / receptor / BMP
Function / homology
Function and homology information


endocardial cushion cell fate commitment / mitral valve morphogenesis / BMP receptor complex / endocardial cushion fusion / atrial septum primum morphogenesis / cardiac muscle cell fate commitment / BMP receptor activity / acute inflammatory response / positive regulation of cardiac epithelial to mesenchymal transition / activin receptor activity, type I ...endocardial cushion cell fate commitment / mitral valve morphogenesis / BMP receptor complex / endocardial cushion fusion / atrial septum primum morphogenesis / cardiac muscle cell fate commitment / BMP receptor activity / acute inflammatory response / positive regulation of cardiac epithelial to mesenchymal transition / activin receptor activity, type I / activin receptor complex / positive regulation of determination of dorsal identity / transforming growth factor beta receptor activity, type I / smooth muscle cell differentiation / endocardial cushion formation / 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 / gastrulation with mouth forming second / dorsal/ventral pattern formation / transforming growth factor beta binding / determination of left/right symmetry / neural crest cell migration / atrioventricular valve morphogenesis / ventricular septum morphogenesis / branching involved in blood vessel morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / 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 / protein serine/threonine kinase activity / protein phosphorylation / 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-protein kinase, active site ...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-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
Chem-QWQ / Activin receptor type-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 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 M4K2153
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
DepositionAug 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jan 31, 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

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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)70,1938
Polymers69,0752
Non-polymers1,1176
Water2,504139
1
A: Activin receptor type I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0343
Polymers34,5381
Non-polymers4972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Activin receptor type I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1585
Polymers34,5381
Non-polymers6214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.650, 85.530, 137.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
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

#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: No special compound details. / 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
#2: Chemical ChemComp-QWQ / 4-methyl-3-[4-(pyrrolidin-1-ylmethyl)phenyl]-5-(3,4,5-trimethoxyphenyl)pyridine


Mass: 418.528 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H30N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
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: 2.65 Å3/Da / Density % sol: 53.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 16% PEG8K, 15% glycerol, 0.08M potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 8, 2018 / Details: Compound Refractive Lenses
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.14→46.09 Å / Num. obs: 39523 / % possible obs: 99.9 % / Observed criterion σ(I): 1.5 / Redundancy: 6.6 % / Biso Wilson estimate: 33.17 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.253 / Rpim(I) all: 0.107 / Rrim(I) all: 0.275 / Χ2: 0.98 / Net I/σ(I): 5.3
Reflection shellResolution: 2.14→2.2 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.747 / Mean I/σ(I) obs: 1 / Num. unique obs: 2862 / CC1/2: 0.542 / Rpim(I) all: 0.937 / Rrim(I) all: 1.901 / Χ2: 0.86 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
xia20.5.48data reduction
Aimless0.7.3data scaling
PHASER2.8.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MTF

3mtf


Resolution: 2.14→46.09 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1991 5.05 %Random selection
Rwork0.2076 37462 --
obs0.2101 39453 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.75 Å2 / Biso mean: 37.704 Å2 / Biso min: 18.68 Å2
Refinement stepCycle: final / Resolution: 2.14→46.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4696 0 162 139 4997
Biso mean--37.61 35.11 -
Num. residues----592
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.14-2.190.38861400.302926252765100
2.19-2.250.31721330.279826502783100
2.25-2.320.33181420.262826382780100
2.32-2.390.34091380.265426432781100
2.39-2.480.36331580.258326272785100
2.48-2.580.35631140.254226732787100
2.58-2.70.3461380.237526472785100
2.7-2.840.26921360.230126742810100
2.84-3.020.28231430.230326442787100
3.02-3.250.27061360.212726902826100
3.25-3.580.24611600.195926732833100
3.58-4.090.20141300.170727092839100
4.09-5.160.19071590.159627202879100
5.16-46.090.21491640.18822849301399

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