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- PDB-5tec: Crystal structure of the TIR domain from the Arabidopsis thaliana... -

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Basic information

Entry
Database: PDB / ID: 5tec
TitleCrystal structure of the TIR domain from the Arabidopsis thaliana NLR protein SNC1
ComponentsProtein SUPPRESSOR OF npr1-1, CONSTITUTIVE 1
KeywordsIMMUNE SYSTEM / TIR domain / plant NLR
Function / homology
Function and homology information


systemic acquired resistance, salicylic acid mediated signaling pathway / response to auxin / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity, cyclic ADP-ribose generating / ADP binding / defense response to bacterium / nucleotide binding / intracellular membrane-bounded organelle / endoplasmic reticulum / ATP binding ...systemic acquired resistance, salicylic acid mediated signaling pathway / response to auxin / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity, cyclic ADP-ribose generating / ADP binding / defense response to bacterium / nucleotide binding / intracellular membrane-bounded organelle / endoplasmic reticulum / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Disease resistance protein RPS4B-like, leucine-rich repeats / 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 ...Disease resistance protein RPS4B-like, leucine-rich repeats / 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 / Winged helix DNA-binding domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein SUPPRESSOR OF npr1-1, CONSTITUTIVE 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhang, X. / Bentham, A. / Ve, T. / Williams, S.J. / Kobe, B.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
Citation
Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Multiple functional self-association interfaces in plant TIR domains.
Authors: Zhang, X. / Bernoux, M. / Bentham, A.R. / Newman, T.E. / Ve, T. / Casey, L.W. / Raaymakers, T.M. / Hu, J. / Croll, T.I. / Schreiber, K.J. / Staskawicz, B.J. / Anderson, P.A. / Sohn, K.H. / ...Authors: Zhang, X. / Bernoux, M. / Bentham, A.R. / Newman, T.E. / Ve, T. / Casey, L.W. / Raaymakers, T.M. / Hu, J. / Croll, T.I. / Schreiber, K.J. / Staskawicz, B.J. / Anderson, P.A. / Sohn, K.H. / Williams, S.J. / Dodds, P.N. / Kobe, B.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2013
Title: Crystallization and preliminary X-ray diffraction analyses of the TIR domains of three TIR-NB-LRR proteins that are involved in disease resistance in Arabidopsis thaliana.
Authors: Wan, L. / Zhang, X. / Williams, S.J. / Ve, T. / Bernoux, M. / Sohn, K.H. / Jones, J.D. / Dodds, P.N. / Kobe, B.
History
DepositionSep 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Mar 22, 2017Group: Database references
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein SUPPRESSOR OF npr1-1, CONSTITUTIVE 1
B: Protein SUPPRESSOR OF npr1-1, CONSTITUTIVE 1


Theoretical massNumber of molelcules
Total (without water)39,6932
Polymers39,6932
Non-polymers00
Water3,711206
1
A: Protein SUPPRESSOR OF npr1-1, CONSTITUTIVE 1


Theoretical massNumber of molelcules
Total (without water)19,8471
Polymers19,8471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein SUPPRESSOR OF npr1-1, CONSTITUTIVE 1


Theoretical massNumber of molelcules
Total (without water)19,8471
Polymers19,8471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.175, 82.175, 124.114
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Protein SUPPRESSOR OF npr1-1, CONSTITUTIVE 1 / AtSNC1 / Disease resistance RPP5-like protein


Mass: 19846.580 Da / Num. of mol.: 2 / Fragment: UNP residues 17-190
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SNC1, BAL, At4g16890, dl4475c, FCAALL.51 / Production host: Escherichia coli (E. coli) / References: UniProt: O23530
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.63 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18%(w/v) PEG 3350, 9%(w/v) glycerol, 0.1 M MMT buffer pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→19.68 Å / Num. obs: 22223 / % possible obs: 99.8 % / Redundancy: 16.7 % / Net I/σ(I): 17.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OZI

3ozi


Resolution: 2.2→19.678 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.95
RfactorNum. reflection% reflection
Rfree0.2168 1081 5.12 %
Rwork0.1782 --
obs0.1801 21119 95.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2436 0 0 206 2642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132481
X-RAY DIFFRACTIONf_angle_d1.2863336
X-RAY DIFFRACTIONf_dihedral_angle_d13.146918
X-RAY DIFFRACTIONf_chiral_restr0.057372
X-RAY DIFFRACTIONf_plane_restr0.008418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.30.35861070.25432235X-RAY DIFFRACTION86
2.3-2.42110.23361390.21232340X-RAY DIFFRACTION91
2.4211-2.57250.25111330.20122393X-RAY DIFFRACTION93
2.5725-2.77060.22541350.18682471X-RAY DIFFRACTION95
2.7706-3.04850.23171420.18422519X-RAY DIFFRACTION97
3.0485-3.48750.19831520.16692585X-RAY DIFFRACTION99
3.4875-4.38590.20451340.14832674X-RAY DIFFRACTION100
4.3859-19.6790.1941390.17952821X-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)
15.3811-1.9573-1.54572.80881.21622.45070.13590.1287-0.0457-0.1414-0.07990.04660.117-0.0797-0.02580.3087-0.00270.00450.2942-0.01660.199232.6031-9.99-24.9164
23.6469-1.1173.06065.989-4.20886.8565-0.21820.6350.4229-1.0273-0.1777-0.9773-0.0969-0.25480.41650.457-0.0317-0.01260.5168-0.01230.475823.9991-11.0854-28.4172
33.0274-0.4218-0.35994.9212-0.7483.57610.09390.09810.29-0.0956-0.05590.0834-0.3037-0.1126-0.0550.28770.03990.01850.3027-0.0170.274526.492.8243-19.3178
44.6665-2.17971.76918.3986-3.34284.44410.0662-0.17850.45720.22570.07870.0934-0.5808-0.6002-0.02010.45880.09830.05120.3634-0.04920.349821.626410.1455-17.8727
52.7695-3.0191-1.57653.43310.95653.12780.4571-0.03050.20310.0628-0.2772-0.0509-0.07470.3468-0.34670.304-0.0260.0120.355-0.01270.236834.8442-6.0564-9.2812
62.20210.7371-0.69972.64871.13343.1889-0.4138-0.51280.1260.1070.1680.37310.2679-0.01940.09210.3815-0.0080.04770.29330.03580.324831.153-15.7653-13.9913
75.9026-0.8543-0.9354.3078-0.78972.4403-0.1022-0.5959-0.19360.0837-0.0473-0.18160.14830.58870.08980.33240.07380.04030.49490.05260.291151.3454-16.2902-18.1114
87.09952.38561.94652.3351.84743.2768-0.995-1.09030.74550.404-0.11370.10390.01811.04020.40230.58490.126-0.04720.78140.23450.689357.1785-23.3838-14.8933
93.93830.7158-0.91233.08760.90821.9110.2155-0.78970.01870.468-0.1772-0.76750.42381.78840.20040.38970.2047-0.11120.64480.00090.367560.7952-14.582-21.5004
103.6387-0.8617-0.69765.2266-0.07061.8723-0.0343-0.56440.16510.1261-0.0991-0.93830.02250.77580.04420.30920.04170.01040.55140.07050.4664.1484-13.1951-26.1929
115.33352.44614.8582.93632.98185.02330.1687-1.44981.6782-0.2708-0.0815-0.6981-1.02020.87450.35260.6602-0.17510.12111.0262-0.21670.892169.05470.5771-23.3624
123.5363-0.2594-0.38843.03730.40063.43780.09160.061-0.1482-0.2011-0.1195-0.45350.21920.48840.01240.31410.06140.03020.34660.01880.338255.9459-15.5481-29.9524
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 45 )
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 123 )
4X-RAY DIFFRACTION4chain 'A' and (resid 124 through 138 )
5X-RAY DIFFRACTION5chain 'A' and (resid 139 through 150 )
6X-RAY DIFFRACTION6chain 'A' and (resid 151 through 166 )
7X-RAY DIFFRACTION7chain 'B' and (resid 12 through 31 )
8X-RAY DIFFRACTION8chain 'B' and (resid 32 through 44 )
9X-RAY DIFFRACTION9chain 'B' and (resid 58 through 71 )
10X-RAY DIFFRACTION10chain 'B' and (resid 72 through 108 )
11X-RAY DIFFRACTION11chain 'B' and (resid 109 through 126 )
12X-RAY DIFFRACTION12chain 'B' and (resid 127 through 166 )

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