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

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Entry
Database: PDB / ID: 7nns
TitleCrystal structure of the ACVR1 (ALK2) kinase in complex with the compound Momelotinib
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 / 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 / negative regulation of signal transduction / BMP signaling pathway / 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
Momelotinib / Activin receptor type-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsWilliams, E. / Chen, Z. / 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 Momelotinib
Authors: Williams, E. / Chen, Z. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.N.
History
DepositionFeb 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 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
B: Activin receptor type I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,99715
Polymers34,5381
Non-polymers1,45914
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Gel filtration confirms behaviour as a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-59 kcal/mol
Surface area13960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.760, 66.760, 147.303
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-701-

HOH

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Components

#1: Protein Activin receptor type I


Mass: 34537.633 Da / Num. of mol.: 1
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
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-C87 / Momelotinib


Mass: 414.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H22N6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.71 Å3/Da / Density % sol: 54.63 % / Description: Single chain in the ASU
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.4M ammonium sulfate, 0.1M tris pH 7.5, 8% glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 14, 2017
RadiationMonochromator: single bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 2.14→53.82 Å / Num. obs: 21731 / % possible obs: 100 % / Redundancy: 9.6 % / Biso Wilson estimate: 27.283 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.24 / Rpim(I) all: 0.081 / Rrim(I) all: 0.253 / Net I/σ(I): 6.9
Reflection shellResolution: 2.14→2.18 Å / Redundancy: 10 % / Rmerge(I) obs: 2.015 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1069 / CC1/2: 0.832 / Rpim(I) all: 0.668 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
xia20.5.161data reduction
xia20.5.161data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H9R

3h9r


Resolution: 2.14→53.82 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2689 1045 4.86 %random selection
Rwork0.2284 20472 --
obs0.2304 21517 99.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.23 Å2 / Biso mean: 28.5963 Å2 / Biso min: 11.24 Å2
Refinement stepCycle: final / Resolution: 2.14→53.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2348 0 148 116 2612
Biso mean--38.34 30.37 -
Num. residues----296
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.14-2.250.42041440.34682839298398
2.25-2.390.37481410.32112864300599
2.39-2.580.34531790.29322845302499
2.58-2.840.29391160.27192930304699
2.84-3.250.28541550.230229113066100
3.25-4.090.23891300.187429933123100
4.1-53.820.19411800.173630903270100

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