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- PDB-6o0w: Crystal structure of the TIR domain from the grapevine disease re... -

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Basic information

Entry
Database: PDB / ID: 6o0w
TitleCrystal structure of the TIR domain from the grapevine disease resistance protein RUN1 in complex with NADP+ and Bis-Tris
ComponentsTIR-NB-LRR type resistance protein RUN1
KeywordsSIGNALING PROTEIN / plant disease resistance
Function / homology
Function and homology information


NADP+ nucleosidase activity / NAD catabolic process / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD+ nucleotidase, cyclic ADP-ribose generating / positive regulation of programmed cell death / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / defense response to fungus / ADP binding / signal transduction ...NADP+ nucleosidase activity / NAD catabolic process / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD+ nucleotidase, cyclic ADP-ribose generating / positive regulation of programmed cell death / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / defense response to fungus / ADP binding / signal transduction / nucleus / cytoplasm
Similarity search - Function
C-JID domain / C-JID 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 4 / Leucine Rich repeats (2 copies) / TIR domain ...C-JID domain / C-JID 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 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-2'-5'-DIPHOSPHATE / Disease resistance protein RUN1
Similarity search - Component
Biological speciesVitis rotundifolia (fox grape)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsHorsefield, S. / Burdett, H. / Zhang, X. / Manik, M.K. / Shi, Y. / Chen, J. / Tiancong, Q. / Gilley, J. / Lai, J. / Gu, W. ...Horsefield, S. / Burdett, H. / Zhang, X. / Manik, M.K. / Shi, Y. / Chen, J. / Tiancong, Q. / Gilley, J. / Lai, J. / Gu, W. / Rank, M. / Casey, L. / Ericsson, D.J. / Foley, G. / Hughes, R.O. / Bosanac, T. / von Itzstein, M. / Rathjen, J.P. / Nanson, J.D. / Boden, M. / Dry, I.B. / Williams, S.J. / Staskawicz, B.J. / Coleman, M.P. / Ve, T. / Dodds, P.N. / Kobe, B.
Funding support Australia, 6items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1107804 Australia
National Health and Medical Research Council (NHMRC, Australia)1160570 Australia
National Health and Medical Research Council (NHMRC, Australia)1071659 Australia
National Health and Medical Research Council (NHMRC, Australia)1108859 Australia
Australian Research Council (ARC)DP160102244 Australia
Australian Research Council (ARC)DP190102526 Australia
CitationJournal: Science / Year: 2019
Title: NAD+cleavage activity by animal and plant TIR domains in cell death pathways.
Authors: Horsefield, S. / Burdett, H. / Zhang, X. / Manik, M.K. / Shi, Y. / Chen, J. / Qi, T. / Gilley, J. / Lai, J.S. / Rank, M.X. / Casey, L.W. / Gu, W. / Ericsson, D.J. / Foley, G. / Hughes, R.O. ...Authors: Horsefield, S. / Burdett, H. / Zhang, X. / Manik, M.K. / Shi, Y. / Chen, J. / Qi, T. / Gilley, J. / Lai, J.S. / Rank, M.X. / Casey, L.W. / Gu, W. / Ericsson, D.J. / Foley, G. / Hughes, R.O. / Bosanac, T. / von Itzstein, M. / Rathjen, J.P. / Nanson, J.D. / Boden, M. / Dry, I.B. / Williams, S.J. / Staskawicz, B.J. / Coleman, M.P. / Ve, T. / Dodds, P.N. / Kobe, B.
History
DepositionFeb 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TIR-NB-LRR type resistance protein RUN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3503
Polymers20,7131
Non-polymers6362
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.085, 79.399, 34.266
Angle α, β, γ (deg.)90.00, 107.42, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein TIR-NB-LRR type resistance protein RUN1


Mass: 20713.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vitis rotundifolia (fox grape) / Gene: RUN1 / Production host: Escherichia coli (E. coli) / References: UniProt: V9M398
#2: Chemical ChemComp-A2P / ADENOSINE-2'-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.16 Å3/Da / Density % sol: 43.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M NaCl, 0.1 M Bis-Tris pH 6.5, 25% w/v PEG 3350) and 10 mM NADP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.75→39.7 Å / Num. obs: 17742 / % possible obs: 99.6 % / Redundancy: 6.9 % / Biso Wilson estimate: 24.8 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.032 / Rrim(I) all: 0.084 / Net I/σ(I): 10.4
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 899 / CC1/2: 0.869 / Rpim(I) all: 0.267 / Rrim(I) all: 0.691 / % possible all: 93.3

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Processing

Software
NameVersionClassification
PHENIX(DEV_3357: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→39.7 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 21.11
RfactorNum. reflection% reflection
Rfree0.195 1775 10.01 %
Rwork0.167 --
obs0.17 17737 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→39.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1390 0 41 54 1485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061474
X-RAY DIFFRACTIONf_angle_d0.7731990
X-RAY DIFFRACTIONf_dihedral_angle_d26.982569
X-RAY DIFFRACTIONf_chiral_restr0.052202
X-RAY DIFFRACTIONf_plane_restr0.005268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.79710.29061300.25261171X-RAY DIFFRACTION95
1.7971-1.850.28511350.21891214X-RAY DIFFRACTION100
1.85-1.90970.27731370.19561234X-RAY DIFFRACTION100
1.9097-1.9780.22741360.1851224X-RAY DIFFRACTION100
1.978-2.05720.23521370.17441231X-RAY DIFFRACTION100
2.0572-2.15080.22221370.17731231X-RAY DIFFRACTION100
2.1508-2.26420.2091380.16941237X-RAY DIFFRACTION100
2.2642-2.4060.22681370.17121230X-RAY DIFFRACTION100
2.406-2.59180.22941360.1981232X-RAY DIFFRACTION100
2.5918-2.85250.21431380.19441240X-RAY DIFFRACTION100
2.8525-3.26510.21071360.18821220X-RAY DIFFRACTION100
3.2651-4.1130.15991370.14651240X-RAY DIFFRACTION100
4.113-39.70970.14281410.13011258X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -17.0323 Å / Origin y: 10.1457 Å / Origin z: 4.3228 Å
111213212223313233
T0.1919 Å20.0082 Å2-0.0018 Å2-0.2151 Å20.026 Å2--0.1646 Å2
L4.7224 °2-1.5668 °2-0.2699 °2-2.4771 °20.1828 °2--1.6376 °2
S-0.1311 Å °-0.3265 Å °-0.0794 Å °0.1187 Å °0.1333 Å °0.1443 Å °0.0019 Å °-0.1088 Å °-0.004 Å °
Refinement TLS groupSelection details: all

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