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- PDB-4c6s: Crystal structure of the TIR domain from the Arabidopsis Thaliana... -

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Basic information

Entry
Database: PDB / ID: 4c6s
TitleCrystal structure of the TIR domain from the Arabidopsis Thaliana disease resistance protein RRS1
ComponentsPROBABLE WRKY TRANSCRIPTION FACTOR 52
KeywordsIMMUNE SYSTEM / PLANT TIR DOMAIN / SIGNAL TRANSDUCTION
Function / homology
Function and homology information


NAD+ nucleosidase activity / ADP binding / defense response / sequence-specific DNA binding / DNA-binding transcription factor activity / signal transduction / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
WRKY domain / WRKY domain superfamily / WRKY DNA -binding domain / WRKY domain profile. / DNA binding domain / Leucine-rich repeat 3 / Leucine Rich Repeat / Toll/interleukin-1 receptor homology (TIR) domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain ...WRKY domain / WRKY domain superfamily / WRKY DNA -binding domain / WRKY domain profile. / DNA binding domain / Leucine-rich repeat 3 / Leucine Rich Repeat / Toll/interleukin-1 receptor homology (TIR) domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Leucine-rich repeat domain superfamily / Winged helix DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Disease resistance protein RRS1 / Disease resistance protein RRS1
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.751 Å
AuthorsWan, L. / Williams, S.J. / Sohn, K.H. / Bernoux, M. / Ma, Y. / Segonzac, C. / Ve, T. / Sarris, P. / Ericsson, D.J. / Saucet, S.B. ...Wan, L. / Williams, S.J. / Sohn, K.H. / Bernoux, M. / Ma, Y. / Segonzac, C. / Ve, T. / Sarris, P. / Ericsson, D.J. / Saucet, S.B. / Zhang, X. / Parker, J. / Dodds, P.N. / Jones, J.D.G. / Kobe, B.
CitationJournal: Science / Year: 2014
Title: Structural Basis for Assembly and Function of a Heterodimeric Plant Immune Receptor.
Authors: Williams, S.J. / Sohn, K.H. / Wan, L. / Bernoux, M. / Sarris, P.F. / Segonzac, C. / Ve, T. / Ma, Y. / Saucet, S.B. / Ericsson, D.J. / Casey, L.W. / Lonhienne, T. / Winzor, D.J. / Zhang, X. / ...Authors: Williams, S.J. / Sohn, K.H. / Wan, L. / Bernoux, M. / Sarris, P.F. / Segonzac, C. / Ve, T. / Ma, Y. / Saucet, S.B. / Ericsson, D.J. / Casey, L.W. / Lonhienne, T. / Winzor, D.J. / Zhang, X. / Coerdt, A. / Parker, J.E. / Dodds, P.N. / Kobe, B. / Jones, J.D.G.
History
DepositionSep 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROBABLE WRKY TRANSCRIPTION FACTOR 52
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6408
Polymers17,1211
Non-polymers5187
Water99155
1
A: PROBABLE WRKY TRANSCRIPTION FACTOR 52
hetero molecules

A: PROBABLE WRKY TRANSCRIPTION FACTOR 52
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,27916
Polymers34,2432
Non-polymers1,03714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_667-y+1,-x+1,-z+5/21
Buried area4060 Å2
ΔGint-149.3 kcal/mol
Surface area14390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.265, 71.265, 66.724
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2004-

HOH

21A-2055-

HOH

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Components

#1: Protein PROBABLE WRKY TRANSCRIPTION FACTOR 52 / DISEASE RESISTANCE PROTEIN RRS1 / DISEASE RESISTANCE PROTEIN SLH1 / PROTEIN SENSITIVE TO LOW ...DISEASE RESISTANCE PROTEIN RRS1 / DISEASE RESISTANCE PROTEIN SLH1 / PROTEIN SENSITIVE TO LOW HUMIDITY 1 / RESISTANCE TO RALSTONIA SOLANACEARUM 1 PROTEIN / WRKY DNA-BINDING PROTEIN 52


Mass: 17121.316 Da / Num. of mol.: 1
Fragment: TOLL/INTERLEUKIN-1 RECEPTOR DOMAIN, RESIDUES 7-153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PMCSG7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q9FH83, UniProt: P0DKH5*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.49 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 7 / Details: 1.8M AMMONIUM SULPHATE, 0.1M BIS-TRIS PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537,1.3776
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
21.37761
ReflectionResolution: 1.75→71.24 Å / Num. obs: 17927 / % possible obs: 100 % / Observed criterion σ(I): 1.7 / Redundancy: 14 % / Biso Wilson estimate: 26.28 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 32.3
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 11.3 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
AutoSolinphasing
PHENIX1.8.2_1309refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RPS4 TIR

Resolution: 1.751→35.632 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 19.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1981 884 4.9 %
Rwork0.1821 --
obs0.1829 17875 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.751→35.632 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1146 0 29 55 1230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071186
X-RAY DIFFRACTIONf_angle_d1.0671600
X-RAY DIFFRACTIONf_dihedral_angle_d14.087438
X-RAY DIFFRACTIONf_chiral_restr0.074179
X-RAY DIFFRACTIONf_plane_restr0.004203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7506-1.86030.23941380.23452770X-RAY DIFFRACTION100
1.8603-2.00390.21481620.19792752X-RAY DIFFRACTION100
2.0039-2.20550.24411360.18152794X-RAY DIFFRACTION100
2.2055-2.52460.22271460.17982825X-RAY DIFFRACTION100
2.5246-3.18040.20981430.18712850X-RAY DIFFRACTION100
3.1804-35.63970.16871590.17283000X-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)
14.3304-4.6031-2.88096.04673.13123.0373-0.35530.02180.54340.00630.2728-0.9336-0.25490.47420.18340.21710.01810.06550.36970.04020.335825.667749.078665.9457
23.79651.90043.1688.2144-0.09443.2864-0.06130.50430.7785-0.2531-0.2323-0.0705-1.15840.32710.20710.31440.0055-0.00860.22470.03740.307618.805259.988475.7545
36.0702-5.3625-6.89015.17346.76788.9102-0.1517-0.1457-0.03430.30130.2447-0.4470.26520.5396-0.08530.1631-0.0039-0.01160.23620.0070.214425.110147.935477.5068
45.08792.0016-0.331.62331.76534.2577-0.10370.59881.1018-0.4352-0.2211-1.0411-0.45860.23860.24580.1647-0.0530.03990.3150.0950.291723.802256.10168.1836
54.23521.6513-2.00991.86770.18024.993-0.04190.9330.5564-0.36980.1479-0.2372-0.36030.274-0.17630.29130.01180.04650.4790.1260.306121.891356.185761.9024
66.27920.8642-2.34575.4554-3.13242.4777-0.20790.37550.8375-0.11530.30080.2111-0.5354-0.2209-0.0920.27050.0266-0.06290.2840.05050.34676.934658.779766.1426
77.68716.26766.99622.01252.98957.75490.141.4744-0.4937-1.39660.2753-1.41930.90241.87080.13770.55770.02640.07530.83470.14710.298817.239852.736255.9449
86.5434-0.7783-0.17194.9585-0.33037.77470.05660.9288-0.175-0.90440.0399-0.37980.11170.0418-0.00910.2709-0.02210.05660.2764-0.01930.19916.445646.366264.0965
93.6417-0.44572.89551.6184-1.14074.182-0.0534-0.262-0.17940.06530.16230.1370.112-0.6039-0.10210.15980.00590.02610.30230.00670.19415.491947.918271.2918
107.7934-3.3294-4.64776.42492.58846.3065-0.26940.4019-0.5244-0.12230.0502-0.08850.73810.10590.21540.23510.02250.0320.1762-0.01270.232120.498839.132973.6286
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 8 THROUGH 15 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 16 THROUGH 22 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 23 THROUGH 34 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 35 THROUGH 46 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 47 THROUGH 68 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 69 THROUGH 81 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 82 THROUGH 90 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 91 THROUGH 101 )
9X-RAY DIFFRACTION9CHAIN A AND (RESID 102 THROUGH 130 )
10X-RAY DIFFRACTION10CHAIN A AND (RESID 131 THROUGH 149 )

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