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- PDB-5ku7: Crystal structure of the TIR domain from the Muscadinia rotundifo... -

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Basic information

Entry
Database: PDB / ID: 5ku7
TitleCrystal structure of the TIR domain from the Muscadinia rotundifolia disease resistance protein RPV1
ComponentsTIR-NB-LRR type resistance protein RPV1
KeywordsSIGNALING PROTEIN / TIR domain / plant NLR
Function / homology
Function and homology information


ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / positive regulation of programmed cell death / defense response to fungus / ADP binding / signal transduction / protein homodimerization activity / nucleus / cytoplasm
Similarity search - Function
Leucine-rich repeat 3 / Leucine Rich Repeat / Toll/interleukin-1 receptor homology (TIR) domain / NB-ARC / NB-ARC domain / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. ...Leucine-rich repeat 3 / Leucine Rich Repeat / Toll/interleukin-1 receptor homology (TIR) domain / NB-ARC / NB-ARC domain / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / 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, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / 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
MALONIC ACID / Disease resistance protein RPV1
Similarity search - Component
Biological speciesVitis rotundifolia (fox grape)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWilliams, S.J. / Ericsson, D.J. / Kobe, B.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP120100685 Australia
Australian Research Council (ARC)DP160102244 Australia
CitationJournal: Front Plant Sci / Year: 2016
Title: Structure and Function of the TIR Domain from the Grape NLR Protein RPV1.
Authors: Williams, S.J. / Yin, L. / Foley, G. / Casey, L.W. / Outram, M.A. / Ericsson, D.J. / Lu, J. / Boden, M. / Dry, I.B. / Kobe, B.
History
DepositionJul 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 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 1.2Oct 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: TIR-NB-LRR type resistance protein RPV1
B: TIR-NB-LRR type resistance protein RPV1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6954
Polymers41,4872
Non-polymers2082
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-14 kcal/mol
Surface area16650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.855, 89.117, 113.858
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein TIR-NB-LRR type resistance protein RPV1


Mass: 20743.279 Da / Num. of mol.: 2 / Fragment: UNP residues 20-193
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vitis rotundifolia (fox grape) / Gene: RPV1 / Production host: Escherichia coli (E. coli) / References: UniProt: V9M2S5
#2: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.57 Å3/Da / Density % sol: 52.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 16% PEG3350, 0.1M Tris pH 8.5 and 2% Tacsimate

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→35.947 Å / Num. obs: 19672 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 27.5 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.091 / Rsym value: 0.036 / Net I/σ(I): 19.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.927 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.784 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4csr

4csr


Resolution: 2.3→35.947 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24
RfactorNum. reflection% reflection
Rfree0.2346 1963 10 %
Rwork0.1799 --
obs0.1853 19625 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 48.9 Å2
Refinement stepCycle: LAST / Resolution: 2.3→35.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2810 0 14 34 2858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082891
X-RAY DIFFRACTIONf_angle_d1.033894
X-RAY DIFFRACTIONf_dihedral_angle_d13.8371072
X-RAY DIFFRACTIONf_chiral_restr0.044400
X-RAY DIFFRACTIONf_plane_restr0.005508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35750.28641380.24281243X-RAY DIFFRACTION100
2.3575-2.42120.29621370.22121231X-RAY DIFFRACTION100
2.4212-2.49250.2911380.23381240X-RAY DIFFRACTION100
2.4925-2.57290.28021370.23091232X-RAY DIFFRACTION100
2.5729-2.66480.27181380.22291242X-RAY DIFFRACTION100
2.6648-2.77150.28031400.21251252X-RAY DIFFRACTION100
2.7715-2.89760.28641380.20591246X-RAY DIFFRACTION100
2.8976-3.05030.29551370.2161238X-RAY DIFFRACTION100
3.0503-3.24130.25841400.19371254X-RAY DIFFRACTION100
3.2413-3.49130.24441420.18341279X-RAY DIFFRACTION100
3.4913-3.84230.24211390.17581258X-RAY DIFFRACTION100
3.8423-4.39740.19411420.14481272X-RAY DIFFRACTION100
4.3974-5.53710.1781440.14531304X-RAY DIFFRACTION100
5.5371-35.95140.20291530.16011371X-RAY DIFFRACTION99
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)
12.04050.4064-0.06014.43780.23312.51240.0184-0.13480.07470.1640.0101-0.2717-0.00090.3121-0.03290.295-0.0139-0.02560.3993-0.02580.37643.727327.229159.3363
23.05340.72150.25784.8423-0.24593.4993-0.0274-0.5727-0.17670.4416-0.0664-0.22890.2620.26920.09280.32320.0450.00040.39090.01980.274242.212918.729469.5324
30.97290.3791-1.27932.0921-3.21666.61330.3483-0.9255-0.30270.4187-0.1768-1.28190.18411.1191-0.07770.70290.1187-0.1370.73880.17630.726550.14749.849874.3709
45.2249-4.27574.04124.6011-4.93397.2166-0.1087-0.676-0.55620.25450.310.60420.026-0.4658-0.2020.3862-0.04380.06930.41730.03940.379530.672620.598968.3136
54.6023.92263.52998.55866.05874.8618-0.065-0.15540.18910.2763-0.22640.2692-0.2247-0.5910.27920.32270.02240.02670.24320.03230.329732.168937.13969.0303
63.04541.1893-0.61992.65030.63781.3123-0.1125-0.07880.1161-0.18650.0010.22920.0575-0.31390.13550.2638-0.0197-0.05520.3858-0.02040.34717.248229.504843.9049
74.6855-1.33740.1596.2286-0.90844.53140.01260.81270.0236-0.4465-0.19540.52420.1123-0.33970.10310.3857-0.0421-0.07460.6282-0.09930.445616.648323.292133.8062
82.19050.71380.30372.96030.91721.5415-0.24460.9087-0.4099-0.67930.08820.11020.2898-0.1948-0.09110.5113-0.0828-0.00540.5584-0.17780.386322.789217.895231.6441
96.9787-5.24834.08019.6552-5.07528.05930.41960.84260-0.1186-0.4544-0.64510.21130.5573-0.01940.2996-0.0092-0.00590.408-0.09350.456736.800328.146545.302
108.1567-0.05670.96716.3589-0.15572.8771-0.27571.28440.5596-0.66130.2418-0.4768-0.67720.0613-0.08430.3642-0.0106-0.0350.30370.03340.381529.10941.926737.2196
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 22:68)
2X-RAY DIFFRACTION2(chain A and resid 69:141)
3X-RAY DIFFRACTION3(chain A and resid 142:149)
4X-RAY DIFFRACTION4(chain A and resid 150:171)
5X-RAY DIFFRACTION5(chain A and resid 172:192)
6X-RAY DIFFRACTION6(chain B and resid 22:83)
7X-RAY DIFFRACTION7(chain B and resid 84:109)
8X-RAY DIFFRACTION8(chain B and resid 110:165)
9X-RAY DIFFRACTION9(chain B and resid 166:178)
10X-RAY DIFFRACTION10(chain B and resid 179:188)

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