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- PDB-8b28: Structure of an intron-retention variant of the plant immune sign... -

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Basic information

Entry
Database: PDB / ID: 8b28
TitleStructure of an intron-retention variant of the plant immune signalling protein EDS1 from Vitis vinifera
ComponentsEnhanced disease susceptibility 1
KeywordsIMMUNE SYSTEM / enhanced disease susceptibility 1 plant innate immune system intron retention during alternative splicing
Function / homology
Function and homology information


defense response / lipid metabolic process / nucleus
Similarity search - Function
EDS1, EP domain / EDS1-like / Enhanced disease susceptibility 1 protein EP domain / Fungal lipase-like domain / Lipase (class 3) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Enhanced disease susceptibility 1
Similarity search - Component
Biological speciesVitis vinifera (wine grape)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsVoss, M. / Niefind, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)NI 643/6-1 Germany
Citation
Journal: Protein Sci. / Year: 2023
Title: A splicing variant of EDS1 from Vitis vinifera forms homodimers but no heterodimers with PAD4.
Authors: Voss, M. / Cseke, L.J. / Gassmann, W. / Niefind, K.
#1: Journal: J Struct Biol / Year: 2019
Title: Arabidopsis immunity regulator EDS1 in a PAD4/SAG101-unbound form is a monomer with an inherently inactive conformation.
Authors: Voss, M. / Toelzer, C. / Bhandari, D.D. / Parker, J.E. / Niefind, K.
History
DepositionSep 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enhanced disease susceptibility 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1459
Polymers43,6491
Non-polymers4978
Water4,792266
1
A: Enhanced disease susceptibility 1
hetero molecules

A: Enhanced disease susceptibility 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,29018
Polymers87,2972
Non-polymers99316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area4670 Å2
ΔGint-2 kcal/mol
Surface area30130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.549, 65.077, 45.454
Angle α, β, γ (deg.)90.000, 105.480, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-643-

HOH

21A-675-

HOH

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Components

#1: Protein Enhanced disease susceptibility 1


Mass: 43648.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vitis vinifera (wine grape) / Gene: EDS1 / Production host: Escherichia coli (E. coli) / References: UniProt: G3F1Q6
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.54 Å3/Da / Density % sol: 51.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein solution: 4.5 mg/ml in 300 mM sodium iodide, 1 % glycerol, 1 mM DTT, 50 mM Hepes buffer, pH 8.0). Reservoir solution: 12 % PEG3350, 300 millimolar CsCl, 100 millimolar Bis-Tris ...Details: Protein solution: 4.5 mg/ml in 300 mM sodium iodide, 1 % glycerol, 1 mM DTT, 50 mM Hepes buffer, pH 8.0). Reservoir solution: 12 % PEG3350, 300 millimolar CsCl, 100 millimolar Bis-Tris puffer, pH 8.5. Crystallization drop before equilibration: 1.5 mikroliter protein solution plus and 1.5 mikroliter reservoir solution.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.915079 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.915079 Å / Relative weight: 1
ReflectionResolution: 1.75→43.81 Å / Num. obs: 29029 / % possible obs: 71.3 % / Redundancy: 2.8 % / Biso Wilson estimate: 22.36 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 5.7
Reflection shellResolution: 1.755→1.942 Å / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1451 / CC1/2: 0.658 / Rsym value: 0.668

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Processing

Software
NameVersionClassification
XDSJan 10, 2022 (BUILT 20220820)data reduction
autoPROC1.0.5data scaling
PHENIX1.20.1_4487phasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6I8G

6i8g


Resolution: 1.75→43.81 Å / SU ML: 0.182 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.538
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2059 1010 3.48 %
Rwork0.1744 28010 -
obs0.1755 29020 71.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.38 Å2
Refinement stepCycle: LAST / Resolution: 1.75→43.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2635 0 32 266 2933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00292758
X-RAY DIFFRACTIONf_angle_d0.56653728
X-RAY DIFFRACTIONf_chiral_restr0.0425398
X-RAY DIFFRACTIONf_plane_restr0.0048492
X-RAY DIFFRACTIONf_dihedral_angle_d12.98231012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.850.2187120.329339X-RAY DIFFRACTION6.08
1.85-1.960.2833550.27131477X-RAY DIFFRACTION26.53
1.96-2.110.26331640.23854508X-RAY DIFFRACTION81
2.11-2.330.25982000.20625511X-RAY DIFFRACTION97.61
2.33-2.660.21471930.18375398X-RAY DIFFRACTION96.81
2.66-3.360.18241920.16475418X-RAY DIFFRACTION96.14
3.36-43.810.18051940.1475359X-RAY DIFFRACTION93.61
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)
14.743322110730.2618849768180.2522914881363.80633949172-0.09909711044024.626962229630.1150102042360.772644974888-0.647339785049-0.635643424456-0.3181150065580.4090738227470.474103588484-0.462182237724-0.05115748872630.1944084903-0.0226203907183-0.003104170242980.2392989616770.01914191085470.10685610355633.078812710613.305648588526.4292727796
22.537749401180.10149954570.8145595663431.858826119-0.242652597841.90791979751-0.105194578933-0.1194862407960.2188853746770.0477985368475-0.008213235683550.0770008147298-0.122945189506-0.08494155331950.06462614271150.09306382439980.02904003027370.03416653707570.0853648370688-0.01650256499090.097098699251230.191492966420.809353368745.2895251878
31.445454990950.444456345484-0.3195697828932.91437324570.1935144971722.616266434880.0937355110818-0.674231059471-0.2071370612720.501985703872-0.0307551699002-0.04476787472330.160565777929-0.20314827573-0.03598004042780.149715890108-0.001337615450370.001089604809040.1806150561360.07264123999090.10837949682832.915793883912.483931200654.605347471
42.43699522807-0.0236737667335-0.2218152352312.0941975355-0.5784954110941.79574651483-0.0459650311869-0.0515005566267-0.0426358109695-0.1134948571730.05413603349350.00167475890170.074111627846-0.1059107393670.02205315771450.05113609984230.01049294755220.005536942088560.06185772456590.01178713821020.057943890363934.029827501314.480514163742.0065702634
52.05214203141-0.7547128495960.1176836585811.33141449126-0.3162305241622.19941536389-0.0671098547415-0.1809610947390.3534183248380.133399988823-0.0156130398281-0.209970392285-0.2685574105930.1406482587110.1048452204940.11926560967-0.0274533316338-0.003816865945560.1697724839670.002891462425370.20343026118150.554909352820.799453805843.4804661976
61.698262258370.1875240466060.05178782285390.0649651984330.3017914962272.28485905004-0.008171261478640.2360689557850.868886057842-0.112708614952-0.123709322176-0.947727022557-0.821053973240.491343002613-0.2641473019190.317381725409-0.1354608902220.1332654589630.2904632900310.1233698511940.63129608849150.505799231331.894078527232.8684944141
74.352931054750.509138769921-1.85057709721.077699754851.98973314095.63444499723-0.01028126991840.5331647239850.0299616607413-0.3347583477890.00699765733925-0.1063105139860.1883574075580.00911829140845-0.06036018784140.2361044737760.006556143884630.05006529676070.2608132472370.05613363405830.1378294955542.00780156616.233754049224.5158273812
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 26 )1 - 261 - 26
22chain 'A' and (resid 27 through 72 )27 - 7227 - 72
33chain 'A' and (resid 73 through 100 )73 - 10073 - 100
44chain 'A' and (resid 101 through 204 )101 - 204101 - 204
55chain 'A' and (resid 205 through 292 )205 - 292205 - 292
66chain 'A' and (resid 293 through 312 )293 - 312293 - 312
77chain 'A' and (resid 313 through 331 )313 - 331313 - 331

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