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- PDB-4c6r: Crystal structure of the TIR domain from the Arabidopsis Thaliana... -

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Basic information

Entry
Database: PDB / ID: 4c6r
TitleCrystal structure of the TIR domain from the Arabidopsis Thaliana disease resistance protein RPS4
ComponentsDISEASE RESISTANCE PROTEIN RPS4
KeywordsIMMUNE SYSTEM / PLANT TIR DOMAIN / SIGNAL TRANSDUCTION
Function / homology
Function and homology information


innate immune response-activating signaling pathway / plant-type hypersensitive response / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity, cyclic ADP-ribose generating / endomembrane system / ADP binding / defense response to bacterium / ATP binding / identical protein binding / nucleus ...innate immune response-activating signaling pathway / plant-type hypersensitive response / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity, cyclic ADP-ribose generating / endomembrane system / ADP binding / defense response to bacterium / ATP binding / identical protein binding / nucleus / membrane / cytoplasm
Similarity search - Function
Leucine-rich repeat 3 / Leucine Rich Repeat / C-JID domain / C-JID domain / Disease resistance protein Roq1-like, winged-helix domain / Toll/interleukin-1 receptor homology (TIR) domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain ...Leucine-rich repeat 3 / Leucine Rich Repeat / C-JID domain / C-JID domain / Disease resistance protein Roq1-like, winged-helix domain / Toll/interleukin-1 receptor homology (TIR) domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Leucine-rich repeat domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Disease resistance protein RPS4
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsWilliams, S.J. / Sohn, K.H. / Wan, L. / Bernoux, M. / Ma, Y. / Segonzac, C. / Ve, T. / Sarris, P. / Ericsson, D.J. / Saucet, S.B. ...Williams, S.J. / Sohn, K.H. / Wan, L. / 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
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DISEASE RESISTANCE PROTEIN RPS4
B: DISEASE RESISTANCE PROTEIN RPS4
C: DISEASE RESISTANCE PROTEIN RPS4
D: DISEASE RESISTANCE PROTEIN RPS4


Theoretical massNumber of molelcules
Total (without water)78,4554
Polymers78,4554
Non-polymers00
Water6,179343
1
A: DISEASE RESISTANCE PROTEIN RPS4


Theoretical massNumber of molelcules
Total (without water)19,6141
Polymers19,6141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DISEASE RESISTANCE PROTEIN RPS4


Theoretical massNumber of molelcules
Total (without water)19,6141
Polymers19,6141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DISEASE RESISTANCE PROTEIN RPS4


Theoretical massNumber of molelcules
Total (without water)19,6141
Polymers19,6141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DISEASE RESISTANCE PROTEIN RPS4


Theoretical massNumber of molelcules
Total (without water)19,6141
Polymers19,6141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.925, 78.637, 80.668
Angle α, β, γ (deg.)65.63, 78.64, 78.93
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9513, -0.2658, 0.1564), (-0.2736, -0.9614, 0.02998), (0.1424, -0.0713, -0.9872)6.722, 98.92, 34.12
2given(-0.9491, 0.2998, -0.09678), (0.2694, 0.613, -0.7427), (-0.1634, -0.7309, -0.6626)60.79, 36.53, 112.3
3given(-0.9995, -0.01386, -0.02914), (-0.01439, -0.6168, 0.787), (-0.02888, 0.787, 0.6162)66.02, 42.54, 56.9

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Components

#1: Protein
DISEASE RESISTANCE PROTEIN RPS4 / TIR-NBS-LRR CLASS DISEASE RESISTANCE PROTEIN


Mass: 19613.748 Da / Num. of mol.: 4
Fragment: TOLL/INTERLEUKIN-1 RECEPTOR DOMAIN, RESIDUES 11-178
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: Q9XGM3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.44 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 6.5
Details: 23% (W/V) PEG 3350, 0.2 M AMMONIUM CITRATE (PH 6.5), 0.2 M SODIUM CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.05→19.6 Å / Num. obs: 43623 / % possible obs: 94 % / Observed criterion σ(I): 5.9 / Redundancy: 3.8 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.6
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5.9 / % possible all: 75.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3OZI

3ozi


Resolution: 2.05→19.598 Å / SU ML: 0.25 / σ(F): 1.98 / Phase error: 23.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2298 1879 4.3 %
Rwork0.1864 --
obs0.1883 43618 94.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.36 Å2
Refinement stepCycle: LAST / Resolution: 2.05→19.598 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5268 0 0 343 5611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085358
X-RAY DIFFRACTIONf_angle_d1.097198
X-RAY DIFFRACTIONf_dihedral_angle_d12.4362068
X-RAY DIFFRACTIONf_chiral_restr0.049817
X-RAY DIFFRACTIONf_plane_restr0.006910
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0501-2.10550.24441230.20412596X-RAY DIFFRACTION75
2.1055-2.16730.27831400.18753229X-RAY DIFFRACTION95
2.1673-2.23720.25141600.18893320X-RAY DIFFRACTION97
2.2372-2.3170.25821470.18483314X-RAY DIFFRACTION97
2.317-2.40960.22851430.18413314X-RAY DIFFRACTION97
2.4096-2.51910.26011520.19163291X-RAY DIFFRACTION98
2.5191-2.65160.27171460.20563302X-RAY DIFFRACTION97
2.6516-2.81730.23651480.1963314X-RAY DIFFRACTION96
2.8173-3.03410.24411430.19693274X-RAY DIFFRACTION96
3.0341-3.33810.26051430.18863262X-RAY DIFFRACTION96
3.3381-3.8180.21991520.18483191X-RAY DIFFRACTION94
3.818-4.79860.1981380.16653174X-RAY DIFFRACTION93
4.7986-19.59920.17491440.18263158X-RAY DIFFRACTION93
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)
13.7457-1.0067-0.5083.95841.28278.34220.07660.2565-0.1001-0.12270.1982-0.6860.2296-0.0552-0.17950.1199-0.00510.04550.1609-0.04480.234930.952123.795129.2856
22.40161.45280.63496.37773.62762.44150.320.126-0.1257-0.4197-0.1523-0.4977-0.34020.2886-0.12480.1050.0480.02120.16780.00030.15427.312515.662326.6334
31.53760.53140.54153.06150.56812.5343-0.12250.12130.1469-0.42550.2322-0.6996-0.2030.7027-0.10480.182-0.00890.09870.2868-0.04940.363435.267325.165527.1882
42.33471.70112.39981.56030.82075.2464-0.32880.550.3679-0.53120.2664-0.6335-0.07210.56330.1080.264-0.09320.19250.29460.00880.544436.029834.698120.9664
54.53160.8672-0.27182.99671.60553.5398-0.18460.24370.4204-0.46490.11570.0006-0.28060.0130.05540.2088-0.00760.0530.12730.03450.206625.877634.001127.2272
62.85540.929-1.23628.67561.59974.0512-0.17180.01720.03280.1308-0.00650.8425-0.2147-0.55050.13490.13620.01920.06660.1793-0.06030.332915.490933.856337.364
73.9019-0.49380.72725.5863-1.81566.2979-0.1639-0.42210.40850.659-0.1058-0.0633-0.4734-0.41560.23660.1820.00390.03860.203-0.11320.327826.667141.592741.0448
86.30235.19264.10835.30534.30955.9798-0.18920.24861.447-0.0486-0.11070.67-0.4885-0.33730.33290.26420.07050.02890.20550.02440.384220.790842.668731.2089
93.36781.3619-0.1012.7775-4.40388.5918-0.1471-0.1614-0.04390.59130.15290.5639-0.692-0.7521-0.0890.20490.02330.05660.1857-0.04490.222514.161523.159832.9145
104.27550.7187-0.9736.5659-4.06422.58750.0020.25450.0816-0.68290.26910.24820.4433-0.3475-0.21670.16060.0113-0.03380.138-0.01840.114418.288118.544422.4983
111.992-0.6671-0.09864.95040.59720.87610.0251-0.1299-0.09120.43340.0742-0.4510.24290.2255-0.0470.14380.0257-0.05550.20760.00480.148243.697765.08939.2505
123.5725-0.01551.15654.69221.0444.36590.11850.0333-0.34870.2775-0.11840.32280.2823-0.23530.00130.1379-0.0207-0.01230.177-0.0070.187132.460355.59863.1306
132.86620.8931-0.36935.1813-3.41647.0323-0.0178-0.08890.10980.03550.00780.26-0.2639-0.3538-0.01160.05750.01480.00270.1565-0.02780.191630.620174.63226.3903
143.47081.18480.79883.3635-1.32715.04770.0254-0.015-0.06870.10550.17240.0133-0.3295-0.2935-0.14040.08340.02770.00490.12770.0060.088639.265942.396571.0365
150.4366-0.58370.00251.7621-1.59364.50260.0349-0.15390.08140.22840.00210.5175-0.1652-0.4977-0.05190.133-0.00740.04160.24040.01350.20134.623347.852966.476
166.5171-0.72923.66865.1647-2.26893.03930.15760.09720.52890.3777-0.01320.2347-0.9775-0.3067-0.10330.19120.06240.05470.2066-0.0180.193837.629157.804563.2397
175.1166-2.3072-1.00613.422-0.3235.8126-0.02710.149-0.07910.1433-0.11190.00370.22470.12850.12990.0363-0.0260.02420.10930.04680.087744.216646.741362.4157
183.78221.50023.94064.03572.02384.2209-0.12070.1660.4446-0.31670.0531-0.1581-0.49820.2670.27150.16590.03580.03120.2190.06380.16845.70654.767858.4354
192.60710.63730.06857.24584.70785.05350.2195-0.36570.0830.1083-0.4985-0.1173-0.2869-0.21630.23080.11350.0099-0.04220.2236-0.020.188350.230947.548366.6799
207.36741.7202-1.2575.47261.09674.80820.2205-0.2163-0.53570.09030.0448-0.84950.21460.7193-0.1390.09610.0381-0.01060.25820.02580.226254.553439.530955.9746
216.4227-3.59492.84467.9561-5.32319.41410.18040.1918-0.2393-0.7181-0.18290.1240.4417-0.18320.08390.11240.03450.00370.1903-0.03150.12546.355541.715348.0093
228.21940.16174.36813.4345-0.65046.26840.0770.1559-0.2784-0.55180.0961-0.37610.19260.3796-0.14090.20720.00860.08250.1697-0.03540.196351.657151.165953.479
237.72640.5766-0.83454.9986-4.20235.4839-0.39480.2683-0.8205-0.8336-0.0287-0.07640.62790.00780.39420.1874-0.020.05220.1482-0.01660.269252.026131.670567.4963
244.1156-0.7297-0.646.9998-0.88063.3869-0.0062-0.18920.18840.92270.0806-0.6054-0.12150.0215-0.11250.15350.0126-0.05950.23330.00060.125350.162341.872976.9148
253.4789-1.2809-1.24844.1806-0.28643.74620.07740.15730.1758-0.09640.0269-0.07990.0868-0.4175-0.0340.0815-0.0502-0.02850.16350.01650.092834.259381.217636.507
262.11620.6989-1.76060.7898-1.0151.6827-0.01380.05360.196-0.14090.18020.23150.1307-0.127-0.12440.1358-0.0426-0.04010.22150.02950.195928.653477.305938.9761
279.0681-2.5588-2.67985.4454.35583.5473-0.32070.3256-0.67130.0613-0.00740.72660.7016-0.63370.25630.171-0.1009-0.02690.23250.03260.274227.522766.946843.3457
282.235-0.35390.03362.41480.7613.9384-0.0397-0.189-0.05650.18050.0703-0.07740.2041-0.0966-0.01770.0896-0.0208-0.0350.14240.03150.130539.624373.865851.3915
294.1106-0.01280.30875.7289-2.11592.5618-0.03390.243-0.0783-0.1047-0.0566-0.3395-0.01270.19940.06380.09090.00010.0360.1526-0.00690.110147.260880.049435.4765
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 15 THROUGH 30 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 31 THROUGH 41 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 42 THROUGH 57 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 58 THROUGH 67 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 68 THROUGH 108 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 109 THROUGH 119 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 120 THROUGH 135 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 136 THROUGH 148 )
9X-RAY DIFFRACTION9CHAIN A AND (RESID 149 THROUGH 159 )
10X-RAY DIFFRACTION10CHAIN A AND (RESID 160 THROUGH 176 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 15 THROUGH 67 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 68 THROUGH 151 )
13X-RAY DIFFRACTION13CHAIN B AND (RESID 152 THROUGH 176 )
14X-RAY DIFFRACTION14CHAIN C AND (RESID 15 THROUGH 42 )
15X-RAY DIFFRACTION15CHAIN C AND (RESID 43 THROUGH 57 )
16X-RAY DIFFRACTION16CHAIN C AND (RESID 58 THROUGH 66 )
17X-RAY DIFFRACTION17CHAIN C AND (RESID 67 THROUGH 82 )
18X-RAY DIFFRACTION18CHAIN C AND (RESID 83 THROUGH 98 )
19X-RAY DIFFRACTION19CHAIN C AND (RESID 99 THROUGH 108 )
20X-RAY DIFFRACTION20CHAIN C AND (RESID 109 THROUGH 119 )
21X-RAY DIFFRACTION21CHAIN C AND (RESID 120 THROUGH 130 )
22X-RAY DIFFRACTION22CHAIN C AND (RESID 131 THROUGH 151 )
23X-RAY DIFFRACTION23CHAIN C AND (RESID 152 THROUGH 159 )
24X-RAY DIFFRACTION24CHAIN C AND (RESID 160 THROUGH 176 )
25X-RAY DIFFRACTION25CHAIN D AND (RESID 15 THROUGH 41 )
26X-RAY DIFFRACTION26CHAIN D AND (RESID 42 THROUGH 57 )
27X-RAY DIFFRACTION27CHAIN D AND (RESID 58 THROUGH 66 )
28X-RAY DIFFRACTION28CHAIN D AND (RESID 67 THROUGH 148 )
29X-RAY DIFFRACTION29CHAIN D AND (RESID 149 THROUGH 176 )

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