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- PDB-5ecq: Crystal Structure of FIN219-FIP1 complex with JA, VAL and ATP -

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Basic information

Entry
Database: PDB / ID: 5ecq
TitleCrystal Structure of FIN219-FIP1 complex with JA, VAL and ATP
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 / toxin catabolic process / L-leucine binding / protein adenylylation / response to mycotoxin / glutathione binding ...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 / toxin catabolic process / L-leucine binding / protein adenylylation / response to mycotoxin / glutathione binding / apoplast / response to UV-B / amino acid binding / response to gravity / glutathione transferase / glutathione transferase activity / glutathione metabolic process / chloroplast / enzyme binding / mitochondrion / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / : / GH3 family central domain / GH3 family C-terminal domain / GH3 family / GH3 family N-terminal domain / 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 ...: / : / GH3 family central domain / GH3 family C-terminal domain / GH3 family / GH3 family N-terminal domain / 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
ADENOSINE-5'-TRIPHOSPHATE / GLUTATHIONE / Chem-JAA / VALINE / 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: 1.66 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)235,20016
Polymers232,3026
Non-polymers2,89810
Water32,9851831
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)117,6008
Polymers116,1513
Non-polymers1,4495
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)117,6008
Polymers116,1513
Non-polymers1,4495
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.844, 53.869, 196.271
Angle α, β, γ (deg.)92.250, 97.170, 113.720
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, 1841 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
#4: Chemical ChemComp-VAL / VALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#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.: 1831 / 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: 45.92 %
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: 1.66→50 Å / Num. obs: 232948 / % possible obs: 95 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.061 / Χ2: 1.003 / Net I/av σ(I): 10.454 / Net I/σ(I): 6.8 / Num. measured all: 424051
Reflection shell

Diffraction-ID: 1 / Redundancy: 1.9 % / Rejects: _

Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
1.66-1.720.414225901.00295.3
1.72-1.790.329226810.98795.5
1.79-1.870.239226151.00495.7
1.87-1.970.165225771.00195.7
1.97-2.090.122226130.98695.5
2.09-2.250.092225880.99795.2
2.25-2.480.072223730.9994.8
2.48-2.840.06224321.00494.6
2.84-3.580.047221451.02594
3.58-500.04220791.03593.4

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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: 1.66→24.535 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 21.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2342 23282 9.99 %
Rwork0.2277 209666 -
obs0.2284 232948 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 34.93 Å2 / Biso mean: 4.0993 Å2 / Biso min: 2 Å2
Refinement stepCycle: final / Resolution: 1.66→24.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15950 0 188 1831 17969
Biso mean--4.84 3.51 -
Num. residues----1994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916544
X-RAY DIFFRACTIONf_angle_d1.83322406
X-RAY DIFFRACTIONf_chiral_restr0.0842246
X-RAY DIFFRACTIONf_plane_restr0.012896
X-RAY DIFFRACTIONf_dihedral_angle_d16.5825952
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 (%)
1.66-1.67890.2057440.19646543728790
1.6789-1.69860.20816870.19256252693990
1.6986-1.71930.19246700.1836663733393
1.7193-1.74110.19958340.19347030786498
1.7411-1.7640.21338070.199469177724100
1.764-1.78810.20887790.194971607939100
1.7881-1.81370.20137410.192369617702100
1.8137-1.84070.19897940.18971987992100
1.8407-1.86950.20737970.183470187815100
1.8695-1.90010.19517830.184770657848100
1.9001-1.93290.20388100.180769837793100
1.9329-1.9680.18467860.174670837869100
1.968-2.00590.17387540.173971217875100
2.0059-2.04680.20078060.189969977803100
2.0468-2.09130.19038020.189970537855100
2.0913-2.13990.20897410.189171217862100
2.1399-2.19340.1937820.198670257807100
2.1934-2.25260.21238090.206971517960100
2.2526-2.31890.21967630.213870177780100
2.3189-2.39360.22777860.214569997785100
2.3936-2.47910.24218120.225470927904100
2.4791-2.57830.22597920.221870537845100
2.5783-2.69550.24497580.23247083784199
2.6955-2.83740.25437750.248270547829100
2.8374-3.01490.28057930.264270197812100
3.0149-3.24720.267730.268169677740100
3.2472-3.57310.28417870.29170667853100
3.5731-4.0880.29817810.30397001778299
4.088-5.14270.32037600.32767019777999
5.1427-24.53750.40547760.43416955773198

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