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- PDB-5ecl: Crystal Structure of FIN219-FIP1 complex with JA, Ile and Mg -

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Basic information

Entry
Database: PDB / ID: 5ecl
TitleCrystal Structure of FIN219-FIP1 complex with JA, Ile and Mg
Components
  • Glutathione S-transferase U20
  • Jasmonic acid-amido synthetase JAR1
KeywordsLIGASE/TRANSFERASE / Jasmonate-amido synthetase / Glutathione S-transferase / Ligase-Transferase complex
Function / homology
Function and homology information


jasmonoyl-L-amino acid ligase / jasmonoyl-L-amino acid ligase activity / regulation of response to red or far red light / cellular response to auxin stimulus / induced systemic resistance, jasmonic acid mediated signaling pathway / response to mycotoxin / toxin catabolic process / L-leucine binding / acid-amino acid ligase activity / protein adenylylation ...jasmonoyl-L-amino acid ligase / jasmonoyl-L-amino acid ligase activity / regulation of response to red or far red light / cellular response to auxin stimulus / induced systemic resistance, jasmonic acid mediated signaling pathway / response to mycotoxin / toxin catabolic process / L-leucine binding / acid-amino acid ligase activity / protein adenylylation / response to gravity / glutathione binding / apoplast / response to UV-B / amino acid binding / glutathione transferase / glutathione transferase activity / glutathione metabolic process / chloroplast / enzyme binding / mitochondrion / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
GH3 family / GH3 auxin-responsive promoter / Glutathione S-transferases Tau, C-terminal alpha helical domain, plant / Glutathione S-transferase Omega/Tau-like / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like ...GH3 family / GH3 auxin-responsive promoter / Glutathione S-transferases Tau, C-terminal alpha helical domain, plant / Glutathione S-transferase Omega/Tau-like / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / ISOLEUCINE / Chem-JAA / Glutathione S-transferase U20 / Jasmonoyl--L-amino acid synthetase JAR1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsChen, C.Y. / Cheng, Y.S.
Citation
Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural basis of jasmonate-amido synthetase FIN219 in complex with glutathione S-transferase FIP1 during the JA signal regulation
Authors: Chen, C.Y. / Ho, S.S. / Kuo, T.Y. / Hsieh, H.L. / Cheng, Y.S.
#1: Journal: Science / Year: 2012
Title: Structural basis for prereceptor modulation of plant hormones by GH3 proteins.
Authors: Westfall, C.S. / Zubieta, C. / Herrmann, J. / Kapp, U. / Nanao, M.H. / Jez, J.M.
History
DepositionOct 20, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Mar 22, 2017Group: Database references
Revision 1.3Nov 8, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Jasmonic acid-amido synthetase JAR1
B: Glutathione S-transferase U20
C: Glutathione S-transferase U20
D: Jasmonic acid-amido synthetase JAR1
E: Glutathione S-transferase U20
F: Glutathione S-transferase U20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,31118
Polymers232,3026
Non-polymers2,00912
Water19,6361090
1
A: Jasmonic acid-amido synthetase JAR1
B: Glutathione S-transferase U20
C: Glutathione S-transferase U20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,1318
Polymers116,1513
Non-polymers9805
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Jasmonic acid-amido synthetase JAR1
E: Glutathione S-transferase U20
F: Glutathione S-transferase U20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,18010
Polymers116,1513
Non-polymers1,0297
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.803, 53.884, 193.165
Angle α, β, γ (deg.)90.070, 90.030, 66.390
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 6 molecules ADBCEF

#1: Protein Jasmonic acid-amido synthetase JAR1 / Jasmonate-amino acid synthetase JAR1 / Protein FAR-RED INSENSITIVE 219 / Protein JASMONATE RESISTANT 1


Mass: 64416.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: JAR1, FIN219, At2g46370, F11C10.6 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9SKE2, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein
Glutathione S-transferase U20 / AtGSTU20 / FIN219-interacting protein 1 / GST class-tau member 20


Mass: 25867.312 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GSTU20, FIP1, At1g78370, F3F9.11 / Plasmid: pRSET-B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8L7C9, glutathione transferase

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Non-polymers , 5 types, 1102 molecules

#3: Chemical ChemComp-JAA / {(1R,2R)-3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl}acetic acid


Mass: 210.270 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H18O3 / Comment: hormone*YM
#4: Chemical ChemComp-ILE / ISOLEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO2
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O6S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1090 / 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: 2.27 Å3/Da / Density % sol: 45.76 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M sodium acetate trihydrate, 0.1 M Tris-HCl, 30%(w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.9762-0.97622
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 8, 2012
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97621
20.976221
ReflectionResolution: 1.85→50 Å / Num. obs: 165367 / % possible obs: 94 % / Redundancy: 2 % / Biso Wilson estimate: 0.57 Å2 / Rmerge(I) obs: 0.085 / Χ2: 0.999 / Net I/av σ(I): 8.178 / Net I/σ(I): 7.1 / Num. measured all: 314260
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.85-1.9220.314162881.00295.8
1.92-1.9920.252163781.00296
1.99-2.0820.206162790.9995.8
2.08-2.1920.165162490.9995.5
2.19-2.3320.133162031.01495
2.33-2.5120.117161121.01394.9
2.51-2.7620.098160370.98594.1
2.76-3.1620.082159890.98493.6
3.16-3.991.90.066156241.02592
3.99-501.90.065149860.98287.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000v708data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.6phasing
PHENIX1.9_1692+svnmodel building
Coot0.8.2model building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EPL

4epl


Resolution: 1.85→24.146 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.56 / Phase error: 18.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2193 16564 10.02 %
Rwork0.2083 148803 -
obs0.2094 165367 97.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 46.1 Å2 / Biso mean: 4.3864 Å2 / Biso min: 2 Å2
Refinement stepCycle: final / Resolution: 1.85→24.146 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15950 0 132 1091 17173
Biso mean--3.22 2.53 -
Num. residues----1994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116480
X-RAY DIFFRACTIONf_angle_d1.96622304
X-RAY DIFFRACTIONf_chiral_restr0.0982386
X-RAY DIFFRACTIONf_plane_restr0.0112892
X-RAY DIFFRACTIONf_dihedral_angle_d18.6555866
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.8710.19715660.18965061562799
1.871-1.8930.20635520.19144989554199
1.893-1.91610.225880.202251645752100
1.9161-1.94030.1955550.195949965551100
1.9403-1.96590.19835560.190150375593100
1.9659-1.99280.20875760.18725165574199
1.9928-2.02120.20485580.18884964552299
2.0212-2.05140.20495510.19585097564899
2.0514-2.08340.19535640.18415100566499
2.0834-2.11760.19015490.18434957550699
2.1176-2.15410.18565740.18155179575399
2.1541-2.19320.19465550.18644948550399
2.1932-2.23540.20435630.19255056561999
2.2354-2.28090.18845550.18914953550899
2.2809-2.33050.18385650.18525069563498
2.3305-2.38470.1935580.17114981553999
2.3847-2.44430.21355590.18685131569098
2.4443-2.51030.19665480.19444818536698
2.5103-2.58410.20045590.20425015557497
2.5841-2.66740.22815410.20165003554498
2.6674-2.76260.22315560.2054864542097
2.7626-2.8730.23045560.20874925548197
2.873-3.00350.20135540.21154982553697
3.0035-3.16160.24285500.2174917546797
3.1616-3.35920.23775370.21184847538496
3.3592-3.61770.20755450.20994849539495
3.6177-3.98030.25755190.22874746526594
3.9803-4.5530.26955290.27274776530593
4.553-5.72360.27535280.27714734526293
5.7236-24.14770.34934980.31134480497888

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