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- PDB-3q4t: Crystal structure of Activin receptor type-IIA (ACVR2A) kinase do... -

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Basic information

Entry
Database: PDB / ID: 3q4t
TitleCrystal structure of Activin receptor type-IIA (ACVR2A) kinase domain in complex with dorsomorphin
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 / odontogenesis of dentin-containing tooth / growth factor binding / 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-TAK / Activin receptor type-2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsChaikuad, A. / Alfano, I. / Mahajan, P. / Cooper, C.D.O. / Sanvitale, C. / Vollmar, M. / Krojer, T. / Muniz, J.R.C. / Raynor, J. / von Delft, F. ...Chaikuad, A. / Alfano, I. / Mahajan, P. / Cooper, C.D.O. / Sanvitale, C. / Vollmar, M. / Krojer, T. / Muniz, J.R.C. / Raynor, J. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Small Molecules Dorsomorphin and LDN-193189 Inhibit Myostatin/GDF8 Signaling and Promote Functional Myoblast Differentiation.
Authors: Horbelt, D. / Boergermann, J.H. / Chaikuad, A. / Alfano, I. / Williams, E. / Lukonin, I. / Timmel, T. / Bullock, A.N. / Knaus, P.
History
DepositionDec 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 10, 2014Group: Database references
Revision 1.3Feb 25, 2015Group: Database references
Revision 1.4Sep 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)75,77830
Polymers73,0982
Non-polymers2,68128
Water8,935496
1
A: Activin receptor type-2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,95515
Polymers36,5491
Non-polymers1,40714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Activin receptor type-2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,82315
Polymers36,5491
Non-polymers1,27414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.100, 110.100, 206.911
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 36548.766 Da / Num. of mol.: 2 / Fragment: kinase domain (UNP residues 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

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Non-polymers , 5 types, 524 molecules

#2: Chemical ChemComp-TAK / 6-[4-(2-piperidin-1-ylethoxy)phenyl]-3-pyridin-4-ylpyrazolo[1,5-a]pyrimidine / Dorsomorphin


Mass: 399.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H25N5O
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 496 / 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: 2.48 Å3/Da / Density % sol: 50.33 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 28% PEG 3350, 0.2M LiSO4, 0.1M Tris, pH 8.8, 10% Ethylene glycol, 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 Q315 3x3 CCD / Detector: CCD / Date: Apr 21, 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: 1.96→48.6 Å / Num. all: 53883 / Num. obs: 53760 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 11.2
Reflection shellResolution: 1.96→2.07 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.783 / Mean I/σ(I) obs: 2.3 / Num. unique all: 7727 / % possible all: 100

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb id 2qlu

2qlu


Resolution: 1.96→45.47 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.75 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IN REFINEMENT BUT NOT OUTPUT TO PDB
RfactorNum. reflection% reflectionSelection details
Rfree0.22301 2733 5.1 %RANDOM
Rwork0.16847 ---
obs0.17124 51027 99.8 %-
all-53760 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.429 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20.42 Å20 Å2
2--0.83 Å20 Å2
3----1.25 Å2
Refine analyzeLuzzati coordinate error obs: 0.209 Å
Refinement stepCycle: LAST / Resolution: 1.96→45.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4857 0 177 496 5530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225174
X-RAY DIFFRACTIONr_bond_other_d0.0010.023578
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.9746958
X-RAY DIFFRACTIONr_angle_other_deg0.9753.0028631
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.325628
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.94324.486243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57315885
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1931529
X-RAY DIFFRACTIONr_chiral_restr0.0990.2732
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025664
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021011
X-RAY DIFFRACTIONr_mcbond_it2.97433065
X-RAY DIFFRACTIONr_mcbond_other0.9631257
X-RAY DIFFRACTIONr_mcangle_it4.4654906
X-RAY DIFFRACTIONr_scbond_it7.17682109
X-RAY DIFFRACTIONr_scangle_it9.781112043
LS refinement shellResolution: 1.96→2.011 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 189 -
Rwork0.26 3713 -
obs--99.95 %
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)
10.61540.27280.92971.52590.56051.4236-0.07080.09330.013-0.12670.06720.0778-0.08730.1340.00360.0459-0.0325-0.02140.12220.02070.0703-15.185262.58765.9993
20.32740.2236-0.03310.49-0.00560.00830.0143-0.05320.015-0.00760.00020.0336-0.01040.019-0.01450.0527-0.0229-0.00220.1237-0.00630.0604-11.006246.692112.2453
30.85240.37780.39431.54090.40741.8710.08480.0068-0.00810.1104-0.03680.03930.1065-0.04-0.04790.0545-0.04420.01060.11560.03020.0454-18.083832.822923.0042
40.1589-0.1028-0.17390.4735-0.04881.3515-0.00260.0108-0.0958-0.02450.0520.04940.0849-0.0271-0.04940.0585-0.0345-0.02190.07580.01220.0885-21.455226.80426.5423
50.31250.56250.23491.19070.72060.6901-0.0128-0.01080.00670.0329-0.03640.03210.0545-0.03330.04920.05320.00040.00690.11260.02240.0689-43.916657.4763-12.1713
60.2931-0.0851-0.18850.5094-0.38770.537-0.0473-0.05360.0109-0.02070.0660.03250.0485-0.0165-0.01870.05850.0171-0.0030.12390.01680.0615-37.867260.15613.2839
72.82430.2908-1.40260.8545-0.29480.767-0.0031-0.20490.395-0.05560.11270.0787-0.01450.0483-0.10970.06530.0625-0.04570.129-0.04730.1972-47.084273.527412.7608
80.5921-0.0635-0.49471.38080.04310.525-0.0951-0.3408-0.07740.00990.00590.02530.03530.17970.08920.06770.09290.0180.29710.01990.0216-47.930256.911621.5462
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B-14 - 214
2X-RAY DIFFRACTION2B215 - 347
3X-RAY DIFFRACTION3B348 - 390
4X-RAY DIFFRACTION4B391 - 485
5X-RAY DIFFRACTION5A-10 - 226
6X-RAY DIFFRACTION6A227 - 347
7X-RAY DIFFRACTION7A348 - 378
8X-RAY DIFFRACTION8A379 - 484

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