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- PDB-7s2z: Crystal structure of the E100A mutant TIR domain from the grapevi... -

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Basic information

Entry
Database: PDB / ID: 7s2z
TitleCrystal structure of the E100A mutant TIR domain from the grapevine disease resistance protein RUN1 bound to NAD
ComponentsDisease resistance protein RUN1
KeywordsSIGNALING PROTEIN / HYDROLASE / NAD+ Hydrolase / Signalling Protein / TIR domain / NAD+ nucleosidase activity
Function / homology
Function and homology information


NADP+ nucleosidase activity / NAD+ nucleosidase activity / NAD+ catabolic process / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity, 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+ nucleosidase activity / NAD+ catabolic process / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity, 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 / : / Disease resistance protein Roq1-like, winged-helix domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / : / Leucine-rich repeat region ...C-JID domain / C-JID domain / : / Disease resistance protein Roq1-like, winged-helix domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / : / Leucine-rich repeat region / 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
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Disease resistance protein RUN1
Similarity search - Component
Biological speciesVitis rotundifolia (muscadine)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsBurdett, H. / Kobe, B.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP160102244 Australia
Australian Research Council (ARC)DP190102526 Australia
CitationJournal: Biorxiv / Year: 2021
Title: Self-association configures the NAD + -binding site of plant NLR TIR domains
Authors: Burdett, H. / Hu, X. / Rank, M.X. / Maruta, N. / Kobe, B.
History
DepositionSep 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Disease resistance protein RUN1
B: Disease resistance protein RUN1
C: Disease resistance protein RUN1
D: Disease resistance protein RUN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,00426
Polymers82,6214
Non-polymers4,38322
Water2,162120
1
A: Disease resistance protein RUN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7997
Polymers20,6551
Non-polymers1,1446
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Disease resistance protein RUN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7997
Polymers20,6551
Non-polymers1,1446
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Disease resistance protein RUN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7036
Polymers20,6551
Non-polymers1,0485
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Disease resistance protein RUN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7036
Polymers20,6551
Non-polymers1,0485
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.743, 116.644, 122.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)

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Components

#1: Protein
Disease resistance protein RUN1 / NAD(+) hydrolase RUN1 / NADP(+) hydrolase RUN1 / Resistance to Uncinula necator protein / MrRUN1


Mass: 20655.346 Da / Num. of mol.: 4 / Mutation: E100A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vitis rotundifolia (muscadine) / Gene: RUN1 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: V9M398, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.58 Å3/Da / Density % sol: 65.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.75 / Details: 2 M ammonium sulfate 0.1 M TrisBase pH 8.75

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.35→47.08 Å / Num. obs: 48034 / % possible obs: 99.8 % / Redundancy: 7.3 % / Biso Wilson estimate: 36.54 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.103 / Net I/σ(I): 13.1
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.753 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4263 / CC1/2: 0.902 / Rrim(I) all: 0.81 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6o0w

6o0w


Resolution: 2.35→47.08 Å / SU ML: 0.2797 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.2117
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2547 2350 4.91 %
Rwork0.2177 45468 -
obs0.2196 47818 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.6 Å2
Refinement stepCycle: LAST / Resolution: 2.35→47.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5602 0 266 120 5988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00335998
X-RAY DIFFRACTIONf_angle_d0.56348116
X-RAY DIFFRACTIONf_chiral_restr0.0389833
X-RAY DIFFRACTIONf_plane_restr0.00361105
X-RAY DIFFRACTIONf_dihedral_angle_d16.0932304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.40.35531380.26752539X-RAY DIFFRACTION97.1
2.4-2.450.3261160.27662648X-RAY DIFFRACTION99.71
2.45-2.510.30161220.2612665X-RAY DIFFRACTION99.54
2.51-2.570.31431460.26412662X-RAY DIFFRACTION99.79
2.57-2.640.3161270.26282644X-RAY DIFFRACTION99.93
2.64-2.720.29051390.24372663X-RAY DIFFRACTION99.79
2.72-2.810.29771340.24812646X-RAY DIFFRACTION99.57
2.81-2.910.28571560.24422637X-RAY DIFFRACTION99.64
2.91-3.020.29991350.25872660X-RAY DIFFRACTION99.64
3.02-3.160.35051370.24492671X-RAY DIFFRACTION99.82
3.16-3.330.25211400.23072690X-RAY DIFFRACTION99.82
3.33-3.540.31350.21732684X-RAY DIFFRACTION99.93
3.54-3.810.22061370.19452703X-RAY DIFFRACTION99.82
3.81-4.190.22441460.17952677X-RAY DIFFRACTION99.65
4.19-4.80.16081410.16172721X-RAY DIFFRACTION99.93
4.8-6.040.20551470.20752745X-RAY DIFFRACTION99.55
6.04-47.080.25181540.2172813X-RAY DIFFRACTION97.7

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