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- PDB-3oom: Crystal structure of the ACVR1 kinase domain in complex with the ... -

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Basic information

Entry
Database: PDB / ID: 3oom
TitleCrystal structure of the ACVR1 kinase domain in complex with the imidazo[1,2-b]pyridazine inhibitor K00507
ComponentsActivin receptor type-1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Protein Kinase / Structural Genomics / Structural Genomics Consortium / SGC / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


endocardial cushion cell fate commitment / mitral valve morphogenesis / endocardial cushion fusion / BMP receptor complex / 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 / endocardial cushion fusion / BMP receptor complex / 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 / positive regulation of determination of dorsal identity / transforming growth factor beta receptor activity, type I / activin receptor complex / 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 / transforming growth factor beta binding / embryonic heart tube morphogenesis / gastrulation with mouth forming second / dorsal/ventral pattern formation / determination of left/right symmetry / neural crest cell migration / atrioventricular valve morphogenesis / 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 / 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 / phosphorylation / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain ...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/tyrosine-protein kinase, catalytic domain / 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. / 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-507 / PHOSPHATE ION / Activin receptor type-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChaikuad, A. / Sanvitale, C. / Cooper, C. / Mahajan, P. / Daga, N. / Petrie, K. / Alfano, I. / Gileadi, O. / Fedorov, O. / Allerston, C. ...Chaikuad, A. / Sanvitale, C. / Cooper, C. / Mahajan, P. / Daga, N. / Petrie, K. / Alfano, I. / Gileadi, O. / Fedorov, O. / Allerston, C. / Krojer, T. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the ACVR1 kinase domain in complex with the imidazo[1,2-b]pyridazine inhibitor K00507
Authors: Chaikuad, A. / Sanvitale, C. / Cooper, C. / Mahajan, P. / Daga, N. / Petrie, K. / Alfano, I. / Gileadi, O. / Fedorov, O. / Allerston, C. / Krojer, T. / von Delft, F. / Weigelt, J. / ...Authors: Chaikuad, A. / Sanvitale, C. / Cooper, C. / Mahajan, P. / Daga, N. / Petrie, K. / Alfano, I. / Gileadi, O. / Fedorov, O. / Allerston, C. / Krojer, T. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.
History
DepositionAug 31, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)35,99519
Polymers34,5381
Non-polymers1,45718
Water4,972276
1
A: Activin receptor type-1
hetero molecules

A: Activin receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,99038
Polymers69,0752
Non-polymers2,91536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1460 Å2
ΔGint-12 kcal/mol
Surface area26610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.400, 88.030, 138.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-142-

HOH

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Components

#1: Protein Activin receptor type-1 / Activin receptor type I / ACTR-I / Serine/threonine-protein kinase receptor R1 / SKR1 / Activin ...Activin receptor type I / ACTR-I / Serine/threonine-protein kinase receptor R1 / SKR1 / Activin receptor-like kinase 2 / ALK-2 / TGF-B superfamily receptor type I / TSR-I


Mass: 34537.633 Da / Num. of mol.: 1 / Fragment: kinase domain (UNP residue 201-499) / Mutation: Q207D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACVR1, ACVRLK2 / Plasmid: pFB-LIC-Bse / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q04771, receptor protein serine/threonine kinase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-507 / 1-{3-[6-(tetrahydro-2H-pyran-4-ylamino)imidazo[1,2-b]pyridazin-3-yl]phenyl}ethanone


Mass: 336.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N4O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O

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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: 52.43 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 3350, 0.2M Na/K PO4, 10% ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 20, 2010 / Details: Kirkpatrick Baez bimorph mirror pair
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2→69.48 Å / Num. all: 24449 / Num. obs: 24402 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 9.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 2 / Num. unique all: 3411 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.6.0066refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H9R

3h9r


Resolution: 2→41.96 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / SU B: 8.378 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IN REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.23095 1237 5.1 %RANDOM
Rwork0.16599 ---
obs0.16937 23165 99.09 %-
all-24402 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.314 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2--1.95 Å20 Å2
3----1.71 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 2→41.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2374 0 95 276 2745
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222584
X-RAY DIFFRACTIONr_bond_other_d0.0010.021783
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.9833489
X-RAY DIFFRACTIONr_angle_other_deg0.9033.0024289
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1345310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02423.982113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32215435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9171516
X-RAY DIFFRACTIONr_chiral_restr0.0930.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212797
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02505
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 68 -
Rwork0.282 1588 -
obs--93.09 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8451-0.5098-0.42081.1185-0.49192.01730.0318-0.02510.03970.0084-0.02950.0442-0.1666-0.2262-0.00230.08370.03410.00270.11720.01250.05851.876826.726623.7687
24.8017-0.1935-2.32361.0317-0.27042.2862-0.00750.18830.08590.05920.0597-0.0252-0.2964-0.4026-0.05220.1120.05870.01940.14710.0090.02313.492128.399525.5476
30.2451-0.0439-0.23470.18470.14281.23530.01450.02180.05050.03180.01560.0189-0.1698-0.0173-0.03010.05660.00170.0030.06430.01690.04216.538725.802618.3211
40.28640.0051-0.05780.1523-0.10650.67090.00450.0372-0.03140.01450.00510.0170.07990.095-0.00960.03940.01810.00490.06080.0010.045319.258512.146314.93
50.2020.53590.10031.9139-0.67271.84630.0210.0491-0.02570.0162-0.0645-0.09580.07560.41930.04340.01060.0355-0.00040.14020.00790.041531.271115.47616.9115
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A202 - 257
2X-RAY DIFFRACTION2A258 - 276
3X-RAY DIFFRACTION3A277 - 334
4X-RAY DIFFRACTION4A335 - 474
5X-RAY DIFFRACTION5A475 - 499

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