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- PDB-6q6z: Structure of the plant immune signaling node EDS1 (enhanced disea... -

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Basic information

Entry
Database: PDB / ID: 6q6z
TitleStructure of the plant immune signaling node EDS1 (enhanced disease susceptibility 1) in complex with nanobody ENB21
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


lipid metabolic process / defense response / 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: 3.476 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
DepositionDec 12, 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

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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)88,6212
Polymers88,6212
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-4 kcal/mol
Surface area33650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.192, 142.192, 97.802
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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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: 15884.468 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)

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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: 3.42 Å3/Da / Density % sol: 64.02 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: CRYSTALLIZATION CONDITIONS: RESERVOIR COMPOSITION (CONDITION A11 of MORPHEUS SCREEN): 20.0 % (V/V) GLYCEROL, 10.0 % (W/V) PEG 4000, 0.03 M MAGNESIUM CHLORIDE, 0.03 M CALCIUM CHLORIDE, 0.0609 ...Details: CRYSTALLIZATION CONDITIONS: RESERVOIR COMPOSITION (CONDITION A11 of MORPHEUS SCREEN): 20.0 % (V/V) GLYCEROL, 10.0 % (W/V) PEG 4000, 0.03 M MAGNESIUM CHLORIDE, 0.03 M CALCIUM CHLORIDE, 0.0609 M TRIS-BASE, 0.0391 M BICINE, PH 8.5; PROTEIN STOCK SOLUTION: 4.1 MG/ML PROTEIN, 50 MM SODIUM CHLORIDE, 1 % (V/V) GLYCEROL, 1 MM DTT, 50 MM HEPES, PH 8.0; DROP COMPOSITION: 150 NL PROTEIN STOCK SOLUTION PLUS 150 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: ESRF / Beamline: ID23-1 / Wavelength: 0.976254 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 3.473→76.586 Å / Num. obs: 12634 / % possible obs: 90.8 % / Redundancy: 19.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.043 / Rrim(I) all: 0.187 / Rsym value: 0.182 / Net I/σ(I): 12.1
Reflection shellResolution: 3.473→3.646 Å / Redundancy: 20.1 % / Num. unique obs: 634 / CC1/2: 0.354 / % possible all: 57.1

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSXDS VERSION JAN 26, 2018, AUTOPROC VERSION JAN 26, 2018data reduction
autoPROCautoPROC (Version 1.0.5), AIMLESS (version 0.7.3), CCP4 7.0.065, STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NFU

4nfu


Resolution: 3.476→61.571 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.268 766 6.08 %
Rwork0.2185 --
obs0.2214 12593 83.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.476→61.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5880 0 0 0 5880
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036011
X-RAY DIFFRACTIONf_angle_d0.7658120
X-RAY DIFFRACTIONf_dihedral_angle_d10.873599
X-RAY DIFFRACTIONf_chiral_restr0.051870
X-RAY DIFFRACTIONf_plane_restr0.0061054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4756-3.7440.3905640.33211223X-RAY DIFFRACTION43
3.744-4.12070.33041520.30512052X-RAY DIFFRACTION75
4.1207-4.71670.29191580.24872819X-RAY DIFFRACTION100
4.7167-5.94180.3131980.25032806X-RAY DIFFRACTION100
5.9418-61.58060.22661940.17862927X-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)
13.277-0.0213-0.15911.5414-1.12212.1687-0.1177-0.19130.45210.14640.3386-0.8837-0.35410.52560.00651.01450.1177-0.04450.9341-0.62691.600532.5646100.0089156.1763
21.67121.02380.05761.6625-0.43490.98090.1080.07750.29990.44510.02220.59240.1984-0.4348-01.14680.28140.11961.0736-0.35020.957313.8578101.0102160.9923
31.90260.2474-0.5823-0.1484-0.50682.02290.2480.10970.2581-0.46160.0112-0.07620.4819-0.05101.45440.2180.26931.0493-0.18540.866231.273977.8485126.9279
40.7280.2482-0.2560.078-0.09650.09270.3152-0.61290.1594-1.2674-0.1406-0.5095-0.008-0.1301-0.03352.53090.2204-0.0341.393-0.55811.999237.1244120.7402182.4673
50.7237-0.0376-0.72770.0521-0.11471.030.518-0.59420.3277-0.2858-0.32510.1926-0.34140.1773-0.12251.95010.3793-0.26331.5952-1.51341.96531.72118.1624198.9839
6-0.0044-0.005-0.00360.00060.0061-0.00080.0190.03741.6730.23990.0861-1.1077-0.1138-0.08730.00012.73220.9361-0.44972.182-0.79662.012830.8273114.5026175.0067
70.50570.1072-0.10860.1538-0.04430.1915-0.10640.2325-0.43730.1548-0.2448-0.52740.3325-0.3291-0.52982.4145-0.3248-1.19780.4432-1.88912.97935.4452108.7204188.9805
81.173-2.03450.09844.0568-1.52823.1342-0.7956-0.3946-0.20210.97480.13290.14820.02340.1507-1.1371.94920.8834-0.57350.6929-0.96542.432938.2854105.3231192.5717
90.07960.04840.16310.0250.10180.2722-0.62210.05020.0120.1227-1.12182.1831-0.00660.6901-0.01271.78840.0619-0.18361.2475-0.38112.32625.8548104.4948191.4999
100.41720.0945-0.59450.06690.04141.59720.46220.90750.36340.06270.63820.5917-0.3267-0.14560.13562.3535-0.6870.35731.8424-0.56392.211624.6383111.9316190.245
110.0601-0.04730.17580.1931-0.31120.6419-0.0912-0.79370.6786-0.9230.0513-0.76290.4182-0.69510.011.68650.1528-0.12791.2171-0.67822.052529.571113.8062195.264
120.0568-0.035-0.18870.02280.12080.588-0.215-0.17680.501-0.40030.1733-0.38730.15140.05490.09662.008-0.1096-1.03181.6076-1.33661.946638.7276112.8192191.3843
130.0845-0.0156-0.43630.0199-0.24552.3417-0.1037-0.93290.2761-0.6273-0.7150.14250.7021.6101-0.43071.66220.4108-0.1931.2791-0.96721.892839.2796113.4153191.1514
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 337 )
3X-RAY DIFFRACTION3chain 'A' and (resid 338 through 616 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 9 )
5X-RAY DIFFRACTION5chain 'B' and (resid 11 through 24 )
6X-RAY DIFFRACTION6chain 'B' and (resid 25 through 37 )
7X-RAY DIFFRACTION7chain 'B' and (resid 38 through 44 )
8X-RAY DIFFRACTION8chain 'B' and (resid 45 through 57 )
9X-RAY DIFFRACTION9chain 'B' and (resid 58 through 75 )
10X-RAY DIFFRACTION10chain 'B' and (resid 76 through 81 )
11X-RAY DIFFRACTION11chain 'B' and (resid 82 through 99 )
12X-RAY DIFFRACTION12chain 'B' and (resid 100 through 105 )
13X-RAY DIFFRACTION13chain 'B' and (resid 106 through 130 )

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