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- PDB-3soc: Crystal structure of Activin receptor type-IIA (ACVR2A) kinase do... -

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Basic information

Entry
Database: PDB / ID: 3soc
TitleCrystal structure of Activin receptor type-IIA (ACVR2A) kinase domain in complex with a quinazolin
ComponentsActivin receptor type-2A
KeywordsTRANSFERASE / Structural Genomics Consortium / SGC / Protein kinase
Function / homology
Function and homology information


Regulation of signaling by NODAL / inhibin-betaglycan-ActRII complex / inhibin binding / penile erection / positive regulation of activin receptor signaling pathway / activin receptor activity / Sertoli cell proliferation / sperm ejaculation / BMP receptor activity / embryonic skeletal system development ...Regulation of signaling by NODAL / inhibin-betaglycan-ActRII complex / inhibin binding / penile erection / positive regulation of activin receptor signaling pathway / activin receptor activity / Sertoli cell proliferation / sperm ejaculation / BMP receptor activity / embryonic skeletal system development / activin receptor complex / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / Signaling by BMP / activin binding / cellular response to BMP stimulus / activin receptor signaling pathway / Signaling by Activin / Signaling by NODAL / gastrulation with mouth forming second / regulation of nitric oxide biosynthetic process / determination of left/right symmetry / anterior/posterior pattern specification / cell surface receptor protein serine/threonine kinase signaling pathway / growth factor binding / odontogenesis of dentin-containing tooth / mesoderm development / positive regulation of SMAD protein signal transduction / BMP signaling pathway / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / coreceptor activity / positive regulation of erythrocyte differentiation / PDZ domain binding / cellular response to growth factor stimulus / : / spermatogenesis / receptor complex / positive regulation of protein phosphorylation / phosphorylation / protein serine/threonine kinase activity / cell surface / positive regulation of transcription by RNA polymerase II / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Activin types I and II receptor domain / Activin types I and II receptor domain / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / 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. ...Activin types I and II receptor domain / Activin types I and II receptor domain / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-GVD / Activin receptor type-2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsChaikuad, A. / Williams, E. / Mahajan, P. / Cooper, C.D.O. / Sanvitale, C. / Vollmar, M. / Muniz, J.R.C. / Yue, W.W. / von Delft, F. / Weigelt, J. ...Chaikuad, A. / Williams, E. / Mahajan, P. / Cooper, C.D.O. / Sanvitale, C. / Vollmar, M. / Muniz, J.R.C. / Yue, W.W. / 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 Activin receptor type-IIA (ACVR2A) kinase domain in complex with a quinazolin
Authors: Chaikuad, A. / Williams, E. / Mahajan, P. / Cooper, C.D.O. / Sanvitale, C. / Vollmar, M. / Muniz, J.R.C. / Yue, W.W. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / ...Authors: Chaikuad, A. / Williams, E. / Mahajan, P. / Cooper, C.D.O. / Sanvitale, C. / Vollmar, M. / Muniz, J.R.C. / Yue, W.W. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A. / Structural Genomics Consortium (SGC)
History
DepositionJun 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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-2A
B: Activin receptor type-2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,54315
Polymers73,0982
Non-polymers1,44613
Water9,728540
1
A: Activin receptor type-2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3038
Polymers36,5491
Non-polymers7547
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Activin receptor type-2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2417
Polymers36,5491
Non-polymers6926
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.680, 110.680, 208.061
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-589-

HOH

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Components

#1: Protein Activin receptor type-2A / Activin receptor type IIA / ACTR-IIA / ACTRIIA


Mass: 36548.766 Da / Num. of mol.: 2 / Fragment: kinase domain (residue 191-488)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACVR2, ACVR2A / Plasmid: pFB-LIC-Bse / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P27037, receptor protein serine/threonine kinase
#2: Chemical ChemComp-GVD / [4-({4-[(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)AMINO]QUINAZOLIN-2-YL}IMINO)CYCLOHEXA-2,5-DIEN-1-YL]ACETONITRILE


Mass: 381.433 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H19N7
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / 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: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG 3350, 0.1M Tris, pH 8.5, 0.2M Ammonium Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 8, 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: 1.95→46.7 Å / Num. all: 55254 / Num. obs: 55250 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 7.7
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.852 / Mean I/σ(I) obs: 2 / Num. unique all: 7889 / % possible all: 99.4

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3Q4T

3q4t


Resolution: 1.95→45.72 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.494 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.14 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS DURING REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.21126 2798 5.1 %RANDOM
Rwork0.16299 ---
obs0.16545 52430 99.39 %-
all-55250 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.327 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20.22 Å20 Å2
2--0.45 Å20 Å2
3----0.67 Å2
Refine analyzeLuzzati coordinate error obs: 0.211 Å
Refinement stepCycle: LAST / Resolution: 1.95→45.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4867 0 102 540 5509
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225196
X-RAY DIFFRACTIONr_bond_other_d0.0010.023533
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.9727028
X-RAY DIFFRACTIONr_angle_other_deg0.9123.0028552
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2825643
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.57824.715246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59615894
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6771527
X-RAY DIFFRACTIONr_chiral_restr0.0950.2747
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025784
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021021
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 168 -
Rwork0.257 3467 -
obs--98.91 %
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)
10.31210.3071-0.26811.9176-1.20121.4691-0.09080.00210.00840.0922-0.0339-0.1041-0.14550.09090.12470.0676-0.0183-0.01970.0686-0.03350.06899.352838.5956-12.9885
20.3499-0.06230.14740.69380.28620.2562-0.0716-0.0586-0.01010.02470.0991-0.0133-0.00830.0261-0.02750.02370.0161-0.01430.081-0.02970.052393.547535.40513.069
30.9980.17580.56731.0625-0.33490.5824-0.0991-0.3312-0.00050.02880.0341-0.1041-0.0589-0.14910.0650.040.073-0.02160.208-0.00510.0354103.101535.765319.7389
46.37871.2315-2.68585.3643-1.09992.25420.01720.17710.0830.01360.0371-0.3262-0.2241-0.0511-0.05430.05130.01360.01090.0565-0.00940.039371.721532.59377.0297
50.45820.3041-0.10130.5228-0.13240.03690.024-0.0236-0.03080.0289-0.0327-0.0513-0.0093-0.00020.00870.0359-0.0090.00720.08090.00760.042666.369948.766712.6532
60.38290.22630.06020.43330.17020.68910.0561-0.01290.13270.02970.03-0.0363-0.05240.008-0.08610.0366-0.01460.02110.0481-0.01220.096375.988967.50110.1925
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 0
2X-RAY DIFFRACTION1A191 - 225
3X-RAY DIFFRACTION2A226 - 347
4X-RAY DIFFRACTION3A348 - 486
5X-RAY DIFFRACTION4B-14 - 0
6X-RAY DIFFRACTION4B191 - 207
7X-RAY DIFFRACTION5B208 - 358
8X-RAY DIFFRACTION6B359 - 486

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