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- PDB-4nfu: Structure of the central plant immunity signaling node EDS1 in co... -

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Basic information

Entry
Database: PDB / ID: 4nfu
TitleStructure of the central plant immunity signaling node EDS1 in complex with its interaction partner SAG101
Components
  • EDS1
  • Senescence-associated carboxylesterase 101
KeywordsSIGNALING PROTEIN / alpha/beta hydrolase fold / innate immunity / pathogen defense / Phytoalexin Deficient 4 / PAD4 / nucleus / hydrolase
Function / homology
Function and homology information


positive regulation of defense response to oomycetes / EDS1 disease-resistance complex / positive regulation of leaf senescence / leaf abscission / systemic acquired resistance, salicylic acid mediated signaling pathway / plant-type hypersensitive response / positive regulation of defense response to bacterium / carboxylesterase / carboxylesterase activity / carboxylic ester hydrolase activity ...positive regulation of defense response to oomycetes / EDS1 disease-resistance complex / positive regulation of leaf senescence / leaf abscission / systemic acquired resistance, salicylic acid mediated signaling pathway / plant-type hypersensitive response / positive regulation of defense response to bacterium / carboxylesterase / carboxylesterase activity / carboxylic ester hydrolase activity / lipid catabolic process / positive regulation of defense response to virus by host / lipid metabolic process / defense response / defense response to Gram-negative bacterium / hydrolase activity / endoplasmic reticulum / membrane / nucleus / cytoplasm
Similarity search - Function
Senescence-associated carboxylesterase 101-like / EDS1, EP domain / EDS1-like / Enhanced disease susceptibility 1 protein EP domain / Fungal lipase-like domain / Lipase (class 3) / Lipases, serine active site. / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
beta-D-glucopyranose / ISOPROPYL ALCOHOL / Senescence-associated carboxylesterase 101 / Protein EDS1L
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.21 Å
AuthorsWagner, S. / Stuttmann, J. / Rietz, S. / Guerois, R. / Niefind, K. / Parker, J.E.
Citation
Journal: Cell Host Microbe / Year: 2013
Title: Structural Basis for Signaling by Exclusive EDS1 Heteromeric Complexes with SAG101 or PAD4 in Plant Innate Immunity.
Authors: Wagner, S. / Stuttmann, J. / Rietz, S. / Guerois, R. / Brunstein, E. / Bautor, J. / Niefind, K. / Parker, J.E.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Crystallization and preliminary crystallographic analysis of Arabidopsis thaliana EDS1, a key component of plant immunity, in complex with its signalling partner SAG101.
Authors: Wagner, S. / Rietz, S. / Parker, J.E. / Niefind, K.
History
DepositionNov 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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: EDS1
B: Senescence-associated carboxylesterase 101
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,2017
Polymers135,6022
Non-polymers5995
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-5 kcal/mol
Surface area50890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.586, 113.643, 125.386
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein EDS1 / Enhanced disease susceptibility 1


Mass: 73152.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: EDS1 / Plasmid: PRSF-DUET-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q9XF23, Hydrolases
#2: Protein Senescence-associated carboxylesterase 101 / Senescence-Associated Protein 101 / SAG101


Mass: 62449.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g14930, F2G14.50, SAG101 / Plasmid: PRSF-DUET-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q4F883, carboxylesterase

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Sugars , 1 types, 1 molecules

#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 306 molecules

#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.95 Å3/Da / Density % sol: 58.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 5% w/v PEG4000, 5% 2-propanol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.0399, 1.0404, 1.0313, 0.9184
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 10, 2009
RadiationMonochromator: Double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.03991
21.04041
31.03131
40.91841
ReflectionResolution: 2.21→35 Å / Num. all: 81125 / Num. obs: 78935 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 43.71 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 21.6
Reflection shellResolution: 2.21→2.25 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.972 / Mean I/σ(I) obs: 2 / Num. unique all: 3608 / Rsym value: 0.972 / % possible all: 79.1

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Processing

Software
NameVersionClassification
SHARPINTEGRATED INTO AUTO-RICKSHAW (EMBL-Hamburg)phasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.21→34.278 Å / SU ML: 0.25 / σ(F): 1.91 / Phase error: 23.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1955 1567 1.99 %
Rwork0.1764 --
obs0.1768 78844 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.21→34.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9277 0 39 302 9618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029544
X-RAY DIFFRACTIONf_angle_d0.62312879
X-RAY DIFFRACTIONf_dihedral_angle_d11.2293592
X-RAY DIFFRACTIONf_chiral_restr0.0231398
X-RAY DIFFRACTIONf_plane_restr0.0031643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.28130.30561210.27695749X-RAY DIFFRACTION81
2.2813-2.36290.30861400.23936439X-RAY DIFFRACTION90
2.3629-2.45740.25031440.21237068X-RAY DIFFRACTION99
2.4574-2.56920.23521360.20797151X-RAY DIFFRACTION100
2.5692-2.70460.25131440.20287146X-RAY DIFFRACTION100
2.7046-2.8740.22381150.1997205X-RAY DIFFRACTION100
2.874-3.09580.23971580.19737195X-RAY DIFFRACTION100
3.0958-3.40710.22741590.1997212X-RAY DIFFRACTION100
3.4071-3.89950.21121360.16687263X-RAY DIFFRACTION100
3.8995-4.91060.14861660.14417281X-RAY DIFFRACTION100
4.9106-34.28240.15121480.15567568X-RAY DIFFRACTION100
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)
14.0166-0.0011-1.82092.53220.79895.95640.0635-0.2437-0.12190.29260.1015-0.03620.34050.0469-0.1020.37620.0243-0.04410.31860.02750.349962.42566.197569.2793
22.2990.20850.32082.3156-0.25754.8630.02670.053-0.0430.02760.2080.18460.1233-0.3215-0.23760.27730.01670.01190.27040.01170.343356.47658.198161.7083
32.39970.4948-0.9242.507-0.23712.37890.0561-0.42-0.00340.36270.058-0.4192-0.23780.7366-0.06630.3721-0.0528-0.04690.6507-0.08460.422878.013716.736166.5128
45.27350.30865.12530.03450.40045.7419-0.2299-0.22390.80290.0201-0.09770.0078-1.0175-0.03370.57770.826-0.11140.02160.4902-0.04880.598967.874732.837555.2166
51.51540.31580.23991.5108-1.29594.03160.01280.1805-0.069-0.17470.1690.18220.2607-0.3802-0.13460.3411-0.0498-0.03030.43910.03630.343750.676318.729328.6571
63.62060.3867-0.21762.86712.01652.78080.06050.0596-0.6692-0.2830.32450.43420.9312-0.4585-0.34980.8368-0.2522-0.21510.61130.10490.711542.88641.790621.2465
72.90420.4274-0.34912.19910.40844.37910.2671-0.2094-0.38750.1442-0.1298-0.00740.50440.1344-0.11870.4583-0.0156-0.10280.45620.02720.437297.941820.805638.3606
81.8609-0.17710.78340.5615-0.13082.80060.15910.0494-0.15930.00990.0164-0.15460.09640.0127-0.18840.3138-0.0046-0.01940.31120.00860.339767.25333.34923.8359
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 70 )
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 184 )
3X-RAY DIFFRACTION3chain 'A' and (resid 185 through 337 )
4X-RAY DIFFRACTION4chain 'A' and (resid 338 through 380 )
5X-RAY DIFFRACTION5chain 'A' and (resid 381 through 524 )
6X-RAY DIFFRACTION6chain 'A' and (resid 525 through 620 )
7X-RAY DIFFRACTION7chain 'B' and (resid -2 through 272 )
8X-RAY DIFFRACTION8chain 'B' and (resid 273 through 537 )

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