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- PDB-4asx: Crystal structure of Activin receptor type-IIA (ACVR2A) kinase do... -

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Basic information

Entry
Database: PDB / ID: 4asx
TitleCrystal structure of Activin receptor type-IIA (ACVR2A) kinase domain in complex with dihydro-Bauerine C
ComponentsACTIVIN RECEPTOR TYPE-2A
KeywordsTRANSFERASE / PROTEIN KINASE
Function / homology
Function and homology information


inhibin binding / Regulation of signaling by NODAL / inhibin-betaglycan-ActRII complex / TGFBR3 regulates activin signaling / penile erection / positive regulation of activin receptor signaling pathway / activin receptor activity / Sertoli cell proliferation / sperm ejaculation / embryonic skeletal system development ...inhibin binding / Regulation of signaling by NODAL / inhibin-betaglycan-ActRII complex / TGFBR3 regulates activin signaling / penile erection / positive regulation of activin receptor signaling pathway / activin receptor activity / Sertoli cell proliferation / sperm ejaculation / embryonic skeletal system development / activin receptor complex / transforming growth factor beta receptor activity, type I / activin receptor activity, type I / activin receptor activity, type II / BMP receptor activity / receptor protein serine/threonine kinase / transforming growth factor beta receptor activity, type II / transmembrane receptor protein serine/threonine kinase activity / transforming growth factor beta receptor activity, type III / activin binding / cellular response to BMP stimulus / Signaling by BMP / activin receptor signaling pathway / pattern specification process / 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 / mesoderm development / odontogenesis of dentin-containing tooth / 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 / osteoblast differentiation / spermatogenesis / positive regulation of protein phosphorylation / receptor complex / protein serine/threonine kinase activity / cell surface / positive regulation of transcription by RNA polymerase II / ATP binding / identical protein 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 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 ...Activin types I and II receptor domain / Activin types I and II receptor domain / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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-6OJ / Activin receptor type-2A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsWilliams, E. / Chaikuad, A. / Canning, P. / Kochan, G. / Mahajan, P. / Cooper, C.D.O. / Beltrami, A. / Krojer, T. / Pohl, B. / Bracher, F. ...Williams, E. / Chaikuad, A. / Canning, P. / Kochan, G. / Mahajan, P. / Cooper, C.D.O. / Beltrami, A. / Krojer, T. / Pohl, B. / Bracher, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / von Delft, F. / Bullock, A.
CitationJournal: To be Published
Title: Crystal Structure of Activin Receptor Type-Iia (Acvr2A) Kinase Domain in Complex with a Beta- Carboline Inhibitor
Authors: Williams, E. / Chaikuad, A. / Canning, P. / Mahajan, P. / Cooper, C.D.O. / Beltrami, A. / Krojer, T. / Huber, K. / Bracher, F. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.
History
DepositionMay 3, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references / Structure summary
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Jun 20, 2018Group: Data collection / Derived calculations / Category: struct_conn
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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)74,19413
Polymers73,0982
Non-polymers1,09711
Water5,783321
1
A: ACTIVIN RECEPTOR TYPE-2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0666
Polymers36,5491
Non-polymers5175
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ACTIVIN RECEPTOR TYPE-2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1287
Polymers36,5491
Non-polymers5796
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.426, 110.426, 208.848
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
11A-2059-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYILEILE5BB-9 - 25015 - 84
21GLYGLYILEILE5AA-9 - 25015 - 84
12SERSERALAALA5BB274 - 349108 - 183
22SERSERALAALA5AA274 - 349108 - 183
13VALVALARGARG5BB360 - 484194 - 318
23VALVALARGARG5AA360 - 484194 - 318
14GLYGLYVALVAL6BB251 - 26185 - 95
24GLYGLYVALVAL6AA251 - 26185 - 95
15ASPASPGLYGLY5BB262 - 27396 - 107
25ASPASPGLYGLY5AA262 - 27396 - 107

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.999578, 0.000187, 0.029032), (0.029032, -0.012558, -0.9995), (0.000178, 0.999921, -0.012558)27.43262, 49.4078, -46.51868

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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, RESIDUES 191-488
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / 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-6OJ / 7,8-bis(chloranyl)-9-methyl-3,4-dihydro-2H-pyrido[3,4-b]indol-1-one / Dihydro-Bauerine C


Mass: 269.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H10Cl2N2O
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.62 Å3/Da / Density % sol: 53.07 % / Description: NONE
Crystal growDetails: 20 % PEG 3350 0.20 M NA(MALONATE)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9611
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9611 Å / Relative weight: 1
ReflectionResolution: 2.05→19.99 Å / Num. obs: 47777 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 8
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 1.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3Q4T

3q4t


Resolution: 2.05→19.99 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.666 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2254 2414 5.1 %RANDOM
Rwork0.18652 ---
obs0.18844 45307 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.745 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.15 Å20 Å2
2--0.31 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.05→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4872 0 70 321 5263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195115
X-RAY DIFFRACTIONr_bond_other_d0.0040.023486
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.9596905
X-RAY DIFFRACTIONr_angle_other_deg1.46638486
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1885628
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.90424.393239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.17915889
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1231529
X-RAY DIFFRACTIONr_chiral_restr0.0880.2735
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025703
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021042
X-RAY DIFFRACTIONr_nbd_refined0.2620.21412
X-RAY DIFFRACTIONr_nbd_other0.2210.23331
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22463
X-RAY DIFFRACTIONr_nbtor_other0.1150.22316
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2125
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0930.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.253
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2450.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7742.9835115
X-RAY DIFFRACTIONr_mcbond_other0.0033.0043486
X-RAY DIFFRACTIONr_mcangle_it2.9124.4276905
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 179 -
Rwork0.27 2921 -
obs--99.65 %
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)
10.41890.2926-0.15630.5027-0.08460.09480.0053-0.0175-0.00750.01170.0178-0.0445-0.0224-0.0092-0.0230.027-0.01180.01260.0563-0.00220.0446-39.323554.999511.4716
20.9466-0.31770.03790.11920.03980.4234-0.146-0.2036-0.00540.04290.08770.0041-0.00420.00170.05830.03630.0215-0.00430.1079-0.02620.029-11.514536.02478.0689
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-9 - 484
2X-RAY DIFFRACTION1A349 - 484
3X-RAY DIFFRACTION2B-9 - 348
4X-RAY DIFFRACTION2B349 - 484

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