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- PDB-3mtf: Crystal structure of the ACVR1 kinase in complex with a 2-aminopy... -

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Basic information

Entry
Database: PDB / ID: 3mtf
TitleCrystal structure of the ACVR1 kinase in complex with a 2-aminopyridine inhibitor
ComponentsActivin receptor type-1
KeywordsTRANSFERASE / Protein Kinase / Structural Genomics / Structural Genomics Consortium / SGC
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-A3F / PHOSPHATE ION / Activin receptor type-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsChaikuad, A. / Sanvitale, C. / Cooper, C. / Mahajan, P. / Daga, N. / Petrie, K. / Alfano, I. / Canning, P. / Krojer, T. / Vollmar, M. ...Chaikuad, A. / Sanvitale, C. / Cooper, C. / Mahajan, P. / Daga, N. / Petrie, K. / Alfano, I. / Canning, P. / Krojer, T. / Vollmar, M. / Knapp, S. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A. / Structural Genomics Consortium (SGC)
CitationJournal: Plos One / Year: 2013
Title: A new class of small molecule inhibitor of BMP signaling.
Authors: Sanvitale, C.E. / Kerr, G. / Chaikuad, A. / Ramel, M.C. / Mohedas, A.H. / Reichert, S. / Wang, Y. / Triffitt, J.T. / Cuny, G.D. / Yu, P.B. / Hill, C.S. / Bullock, A.N.
History
DepositionApr 30, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 18, 2014Group: Database references
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

Downloads & links

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Assembly

Deposited unit
A: Activin receptor type-1
B: Activin receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,59529
Polymers69,0752
Non-polymers2,52027
Water6,864381
1
A: Activin receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,89116
Polymers34,5381
Non-polymers1,35315
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Activin receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,70413
Polymers34,5381
Non-polymers1,16712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.688, 138.255, 59.934
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

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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.: 2 / Fragment: kinase domain (UNP residues 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.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-A3F / 3-[6-amino-5-(3,4,5-trimethoxyphenyl)pyridin-3-yl]phenol


Mass: 352.384 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H20N2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 2.51 Å3/Da / Density % sol: 50.99 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.6M Na/KPO4, 0.1M HEPES 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: I04 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 3, 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: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.15→41.85 Å / Num. all: 37445 / Num. obs: 35528 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.155 / Net I/σ(I): 10.5
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.638 / Mean I/σ(I) obs: 2.9 / Num. unique all: 4945 / % possible all: 90.5

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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: 2.15→41.85 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / SU B: 11.71 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24421 1911 5.1 %RANDOM
Rwork0.18201 ---
obs0.18523 35528 96.92 %-
all-37445 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.703 Å2
Baniso -1Baniso -2Baniso -3
1-2.57 Å20 Å20 Å2
2---1.77 Å20 Å2
3----0.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.249 Å
Refinement stepCycle: LAST / Resolution: 2.15→41.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4718 0 160 381 5259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224977
X-RAY DIFFRACTIONr_bond_other_d0.0010.023368
X-RAY DIFFRACTIONr_angle_refined_deg1.6031.9726728
X-RAY DIFFRACTIONr_angle_other_deg0.7783.0018160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0085596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62823.709213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.03115839
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1351532
X-RAY DIFFRACTIONr_chiral_restr0.0850.2743
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025380
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02982
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
793tight positional0.120.05
3168medium positional0.390.5
793tight thermal2.060.5
3168medium thermal3.812
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 124 -
Rwork0.239 2366 -
obs--89.28 %
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)
10.41370.72650.08981.5077-0.25760.76430.0384-0.0195-0.04370.0816-0.0701-0.0993-0.00650.06160.03170.06460.0157-0.02870.06960.01390.0688-17.4639-21.04443.7239
20.28790.3018-0.06071.4479-0.55080.2564-0.0123-0.0218-0.0443-0.0039-0.0847-0.1722-0.01850.07610.0970.0546-0.0046-0.00480.08250.03490.0754-15.827-17.550132.1357
30.24920.18540.02170.639-0.06180.0722-0.0362-0.0060.0231-0.18710.0241-0.00330.03460.04520.01210.1110.0023-0.01920.0450.00480.03-29.231-14.256722.6022
40.6038-0.8459-0.1361.44570.12050.1701-0.0280.05440.00290.030.02130.0228-0.03350.0240.00680.0692-0.01160.0190.08660.01090.0435-15.888-43.938-13.5167
50.2339-0.23320.19190.8997-0.88031.0614-0.02380.0131-0.0047-0.0053-0.0234-0.1001-0.00570.08890.04720.06420.00470.00270.0607-0.00350.0422-14.4165-48.1405-2.0857
60.12420.01360.07040.8812-0.58640.65130.00360.0128-0.01530.06490.0960.1215-0.0216-0.0763-0.09960.07240.01770.01590.06770.01470.0458-27.3356-53.38327.0006
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A203 - 257
2X-RAY DIFFRACTION2A258 - 329
3X-RAY DIFFRACTION3A330 - 498
4X-RAY DIFFRACTION4B202 - 257
5X-RAY DIFFRACTION5B258 - 329
6X-RAY DIFFRACTION6B330 - 499

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