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- PDB-6i8g: Structure of the plant immune signaling node EDS1 (enhanced disea... -

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Basic information

Entry
Database: PDB / ID: 6i8g
TitleStructure of the plant immune signaling node EDS1 (enhanced disease susceptibility 1) in complex with nanobody ENB73
Components
  • EDS1-specific nanobody
  • Protein EDS1L
KeywordsIMMUNE SYSTEM / enhanced disease susceptibility 1 / plant innate immune system / alpha/beta hydrolase fold / nanobody
Function / homology
Function and homology information


defense response / lipid metabolic process / hydrolase activity / endoplasmic reticulum / nucleus
Similarity search - Function
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
Biological speciesArabidopsis thaliana (thale cress)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.344 Å
AuthorsNiefind, K. / Voss, M. / Toelzer, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationNI 643/6-1 Germany
Citation
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.
#1: 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.
#2: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
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.
#3: Journal: New Phytol. / Year: 2011
Title: Different roles of Enhanced Disease Susceptibility1 (EDS1) bound to and dissociated from Phytoalexin Deficient4 (PAD4) in Arabidopsis immunity.
Authors: Rietz, S. / Stamm, A. / Malonek, S. / Wagner, S. / Becker, D. / Medina-Escobar, N. / Vlot, A.C. / Feys, B.J. / Niefind, K. / Parker, J.E.
History
DepositionNov 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Data collection / Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 1.2Dec 4, 2019Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / software
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein EDS1L
B: EDS1-specific nanobody


Theoretical massNumber of molelcules
Total (without water)88,6172
Polymers88,6172
Non-polymers00
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-4 kcal/mol
Surface area33360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.504, 68.232, 105.273
Angle α, β, γ (deg.)90.00, 123.44, 90.00
Int Tables number5
Space group name H-MC121
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

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Components

#1: Protein Protein EDS1L / Enhanced disease susceptibility 1-like


Mass: 72736.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: EDS1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9XF23
#2: Antibody EDS1-specific nanobody


Mass: 15880.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.13 Å3/Da / Density % sol: 60.7 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: Reservoir composition: 17.5 % (w/v) PEG3350, 0.2 M sodium citrate, 0.1 M Bis-Tris buffer, pH 8.5; Protein stock solution: 2.8 mg/ml protein in 50 mM sodium chloride, 1 % (v/v) glycerole, 1mM ...Details: Reservoir composition: 17.5 % (w/v) PEG3350, 0.2 M sodium citrate, 0.1 M Bis-Tris buffer, pH 8.5; Protein stock solution: 2.8 mg/ml protein in 50 mM sodium chloride, 1 % (v/v) glycerole, 1mM DTT, 50 mM HEPES, pH 8.0; drop composition: 1 mikroliter protein stock solution + 1 mikroliter reservoir solution; crystals were cryoprotected in 17.5 % (w/v) PEG3350, 20 % (v/v) ethylene glycol, 0.2 M sodium citrate, 0.1 M Bis-Tris buffer, pH 8.5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jan 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.344→83.773 Å / Num. obs: 31550 / % possible obs: 71.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 8
Reflection shellResolution: 2.344→2.565 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1577 / Rsym value: 0.87 / % possible all: 15.1

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSVERSION Jan 26, 2018data reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
autoPROCdata reduction
autoPROCVersion 1.0.5data scaling
STARANISOdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NFU

4nfu


Resolution: 2.344→52.57 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.74
RfactorNum. reflection% reflection
Rfree0.222 1295 4.11 %
Rwork0.194 --
obs0.195 31537 71.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.344→52.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5980 0 0 169 6149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026138
X-RAY DIFFRACTIONf_angle_d0.5228302
X-RAY DIFFRACTIONf_dihedral_angle_d15.3963680
X-RAY DIFFRACTIONf_chiral_restr0.04890
X-RAY DIFFRACTIONf_plane_restr0.0041079
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.344-2.43780.344540.2912243X-RAY DIFFRACTION5
2.4378-2.54870.328630.3096998X-RAY DIFFRACTION22
2.5487-2.68310.3319910.28712407X-RAY DIFFRACTION51
2.6831-2.85120.29441570.28853433X-RAY DIFFRACTION73
2.8512-3.07130.28791820.27364461X-RAY DIFFRACTION94
3.0713-3.38040.26951980.2354663X-RAY DIFFRACTION99
3.3804-3.86940.24421990.1934620X-RAY DIFFRACTION98
3.8694-4.87450.18451990.14374569X-RAY DIFFRACTION96
4.8745-52.58330.15942020.15374848X-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)
11.9118-0.7885-0.58381.78590.48712.5561-0.08790.0635-0.20170.09210.07620.02620.30750.0365-0.00830.2258-0.0329-0.00810.1315-0.00580.2307140.9226-30.7636104.9686
22.36730.2222-0.54152.86860.58680.8199-0.109-0.1631-0.11060.19020.2694-0.52270.14250.64170.03380.30150.0939-0.07140.4677-0.07690.3901159.5783-31.2154110.2968
32.0865-0.07131.11290.7598-0.09413.4215-0.02170.67960.346-0.1395-0.04320.0105-0.07030.3494-0.01570.2687-0.00520.07310.43440.09320.4483143.6273-15.826472.8895
40.2691-0.14220.04950.0522-0.00880.09450.26-0.09240.26150.054-0.25940.1121-0.60050.05810.00090.6670.00490.01780.2444-0.01420.2667136.9273-32.0743148.3217
50.14650.05950.20970.231-0.41571.5826-0.2272-0.1322-0.0166-0.10270.18230.4133-0.5762-0.48980.00390.50620.0473-0.08350.1896-0.00180.3694134.1452-31.9076136.3049
60.3401-0.0121-0.52760.00070.01780.80220.1772-0.3523-0.0150.2235-0.1051-0.2543-0.4790.597-0.01680.5125-0.1584-0.04410.3568-0.01490.316146.2132-37.1055143.5073
70.1034-0.00260.00960.0036-0.05580.72810.01930.1789-0.5034-0.29190.46910.27080.37390.23110.010.563-0.0459-0.07820.27340.00620.4247138.5526-43.3439131.3518
80.1560.1288-0.06740.1467-0.06780.18660.169-0.06620.02-0.4179-0.16980.2629-0.2354-0.0681-0.00030.4926-0.0063-0.04630.24510.07240.3376134.6268-40.6225142.0638
90.31830.123-0.210.0731-0.17930.33910.4382-0.1260.1176-0.104-0.30120.0897-0.42150.28910.01340.434-0.02360.01310.1997-0.01550.3223144.2069-38.3669142.9939
100.2941-0.14190.06260.20680.11860.26930.2556-0.33950.46510.1362-0.1329-0.2885-0.38750.11010.02180.6282-0.0870.00150.29670.01670.3872144.2898-33.105146.5476
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 2 THROUGH 211 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 212 THROUGH 325 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 326 THROUGH 619 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 1 THROUGH 17 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 18 THROUGH 32 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 33 THROUGH 51 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 52 THROUGH 60 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 61 THROUGH 83 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 84 THROUGH 107 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 108 THROUGH 126 )

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