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- PDB-6i8h: Structure of the plant immune signaling node EDS1 (enhanced disea... -

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Basic information

Entry
Database: PDB / ID: 6i8h
TitleStructure of the plant immune signaling node EDS1 (enhanced disease susceptibility 1) in complex with nanobody ENB15
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: 3.682 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 6, 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)87,7122
Polymers87,7122
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-5 kcal/mol
Surface area33470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.887, 145.887, 152.770
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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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: 14975.403 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)
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: 2.66 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Reservoir composition: 12.5 % (v/v) (RS)-2-methyl-2,4-pentanediol, 12.5 % (w/v) PEG 1000, 12.5 % (w/v) PEG3350, 0.03 M magnesium chloride, 0.03 M calcium chloride, 0.0612 M MES, 0.0388 M ...Details: Reservoir composition: 12.5 % (v/v) (RS)-2-methyl-2,4-pentanediol, 12.5 % (w/v) PEG 1000, 12.5 % (w/v) PEG3350, 0.03 M magnesium chloride, 0.03 M calcium chloride, 0.0612 M MES, 0.0388 M imidazole, pH 6.5; protein stock solution: 4.1 mg/ml protein, 50 mM sodium chloride, 1 % (v/v) glycerole, 1 mM DTT, 50 mM HEPES, pH 8.0; drop composition: 150 nl protein stock solution plus 225 nl reservoir solution; cryo conditions: the crystals were flash frozen directly from the equilibrated crystallization drops.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.682→97.361 Å / Num. obs: 8246 / % possible obs: 93 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 9.8
Reflection shellResolution: 3.682→4.05 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.349 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 411 / Rsym value: 1.349 / % possible all: 59.5

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Processing

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

4nfu


Resolution: 3.682→72.94 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.75
RfactorNum. reflection% reflection
Rfree0.287 800 9.71 %
Rwork0.242 --
obs0.246 8238 75.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.682→72.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5893 0 0 0 5893
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026024
X-RAY DIFFRACTIONf_angle_d0.6088138
X-RAY DIFFRACTIONf_dihedral_angle_d11.0163609
X-RAY DIFFRACTIONf_chiral_restr0.041869
X-RAY DIFFRACTIONf_plane_restr0.0051058
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6815-3.9122000.389126X-RAY DIFFRACTION7
3.9122-4.21420.3952800.323722X-RAY DIFFRACTION45
4.2142-4.63820.31331600.29531566X-RAY DIFFRACTION97
4.6382-5.30920.34052000.28531595X-RAY DIFFRACTION100
5.3092-6.68840.34681600.2861674X-RAY DIFFRACTION100
6.6884-72.95780.24052000.19541755X-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)
14.05631.0235-0.45571.4636-1.46191.70690.60020.88022.09970.6159-0.04350.1064-1.6114-0.35470.21781.30890.31580.44751.22450.07541.57852.7833-43.303611.4332
22.16660.49040.24792.21920.31961.92520.528-0.69410.36570.8778-0.18180.1705-0.5185-0.32830.28930.8860.08930.3091.69930.07591.466-5.4871-58.452715.0646
32.43440.8838-1.76571.6657-1.74981.1986-0.43090.993-0.479-0.74510.3051-0.54910.238-0.17220.00841.3752-0.25920.12811.3848-0.05790.802220.1205-60.2724-17.6158
4-0.0153-0.02270.01390.0061-0.06250.06860.26840.5159-0.1729-0.1278-0.2236-0.3134-0.1189-0.2640.00072.13910.5876-0.25571.84630.0782.375-14.8184-23.7914-15.619
50.20090.2029-0.1930.1765-0.20440.25410.3026-0.3527-0.1236-1.6989-0.4263-0.9207-1.85940.6329-0.0041.74160.4774-0.16061.6041-0.14742.4918-3.5245-27.3914-6.2592
60.05820.03040.03230.00490.00850.0101-0.60720.3946-0.13410.54330.3668-0.48511.6015-1.19220.00032.5793-0.1567-0.5152.1265-0.75922.6931-13.9496-36.8433-17.4982
70.04940.07720.05620.18360.14170.20220.37020.0989-0.0662-1.7209-0.5614-0.41441.1837-0.2297-0.21171.4044-0.0831-0.22591.62450.54953.1242-7.1811-36.8861-17.0581
81.1493-0.9910.19620.8431-0.19680.36640.9316-0.79470.30780.0823-1.0957-1.28660.867-0.4771-0.00071.328-0.4499-0.2261.5979-0.1382.11380.0028-33.0269-21.0632
90.12210.0493-0.09850.0308-0.08540.253-0.4512-0.4921-0.2404-0.1879-0.3205-0.07080.04260.0376-1.03730.23810.2984-0.20212.39060.38362.6895-2.7664-24.3158-13.0814
100.2611-0.0763-0.25760.13340.0330.2061-1.4013-0.4646-0.62060.271-0.12670.27661.8284-0.7425-0.02982.5510.099-0.13992.460.20641.5421-14.0999-29.7933-21.9121
113.7348-1.857-0.2546.6185.11184.3829-1.34140.37270.7270.2923-1.78431.60790.5666-1.1377-1.44051.68620.19540.46472.07460.63432.4886-6.2-37.879-5.2826
120.02580.00620.02950.012-0.03350.1224-0.4880.2154-0.24020.52170.1367-0.60970.2474-0.11820.00042.53130.2632-0.06791.97420.14111.7623-19.7561-26.4931-22.0896
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 3 THROUGH 139 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 140 THROUGH 337 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 338 THROUGH 620 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 3 THROUGH 17 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 18 THROUGH 34 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 35 THROUGH 44 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 45 THROUGH 51 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 52 THROUGH 67 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 68 THROUGH 83 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 84 THROUGH 96 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 97 THROUGH 111 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 112 THROUGH 118 )

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