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- PDB-7jlv: Structure of the activated Roq1 resistosome directly recognizing ... -

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Basic information

Entry
Database: PDB / ID: 7jlv
TitleStructure of the activated Roq1 resistosome directly recognizing the pathogen effector XopQ
ComponentsDisease resistance protein Roq1
KeywordsIMMUNE SYSTEM / Resistosome / Plant Immunity / Effector / LRR / TIR / NB-ARC
Function / homology
Function and homology information


ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity, cyclic ADP-ribose generating / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / defense response / ADP binding / signal transduction
Similarity search - Function
Disease resistance protein RPS4B-like, leucine-rich repeats / 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 / TIR domain / Toll - interleukin 1 - resistance ...Disease resistance protein RPS4B-like, leucine-rich repeats / 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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Disease resistance protein Roq1
Similarity search - Component
Biological speciesNicotiana benthamiana (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsMartin, R. / Qi, T. / Zhang, H. / Lui, F. / King, M. / Toth, C. / Nogales, E. / Staskawicz, B.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Science / Year: 2020
Title: Structure of the activated ROQ1 resistosome directly recognizing the pathogen effector XopQ.
Authors: Raoul Martin / Tiancong Qi / Haibo Zhang / Furong Liu / Miles King / Claire Toth / Eva Nogales / Brian J Staskawicz /
Abstract: Plants and animals detect pathogen infection using intracellular nucleotide-binding leucine-rich repeat receptors (NLRs) that directly or indirectly recognize pathogen effectors and activate an ...Plants and animals detect pathogen infection using intracellular nucleotide-binding leucine-rich repeat receptors (NLRs) that directly or indirectly recognize pathogen effectors and activate an immune response. How effector sensing triggers NLR activation remains poorly understood. Here we describe the 3.8-angstrom-resolution cryo-electron microscopy structure of the activated ROQ1 (recognition of XopQ 1), an NLR native to with a Toll-like interleukin-1 receptor (TIR) domain bound to the effector XopQ ( outer protein Q). ROQ1 directly binds to both the predicted active site and surface residues of XopQ while forming a tetrameric resistosome that brings together the TIR domains for downstream immune signaling. Our results suggest a mechanism for the direct recognition of effectors by NLRs leading to the oligomerization-dependent activation of a plant resistosome and signaling by the TIR domain.
History
DepositionJul 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 6, 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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Assembly

Deposited unit
A: Disease resistance protein Roq1
B: Disease resistance protein Roq1
D: Disease resistance protein Roq1
G: Disease resistance protein Roq1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)604,72012
Polymers602,5944
Non-polymers2,1268
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "D"
d_4ens_1chain "G"
d_1ens_2chain "E"
d_2ens_2chain "C"
d_3ens_2chain "F"
d_4ens_2chain "H"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASPLEUA1 - 437
d_21ens_1ASPLEUD1 - 437
d_31ens_1ASPLEUG1 - 437
d_41ens_1ASPLEUJ1 - 437
d_11ens_2ATPATPB
d_21ens_2ATPATPE
d_31ens_2ATPATPH
d_41ens_2ATPATPK

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.000295722460157, 0.999999830019, 0.000502503217476), (-0.999999830836, 0.000295470693947, 0.000501024470432), (0.000500875910293, -0.000502651296659, 0.999999748232)-0.0540097561364, 121.987688498, -0.0245218043095
2given(-0.999999979976, -0.000200118624734), (-0.999999280273, -0.00119977208537), (-0.000200118152072, -0.00119977216421, 0.999999260249)122.022119037, 122.083835207, 0.070285350064
3given(-0.00126119756338, -0.999999149411, -0.000332501802043), (0.999999197956, -0.00126123607371, 0.000115635668289), (-0.000116054933198, -0.000332355695939, 0.999999938035)122.162205313, 0.0564994868042, 0.0333646394299
4given(0.00407087051541, -0.999988437717, 0.0025597746417), (0.999779511587, 0.00412272532222, 0.020589593165), (-0.02059990835, 0.00247539267331, 0.999784734934)121.625475962, -1.57603314189, 0.825261137361
5given(-0.999337651468, -0.0176388478685, 0.0318296937496), (0.0185554364899, -0.999414832078, 0.0287348081461), (0.0313042191244, 0.0293063895489, 0.999080167653)121.312968251, 119.292055918, -3.55652107331
6given(-0.0259307623064, 0.999527230909, -0.0165199950671), (-0.998251363815, -0.0250124455646, 0.053559240185), (0.0531207135543, 0.0178799395325, 0.998428013206)2.22776316267, 120.513381173, -3.65117543031

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Components

#1: Protein
Disease resistance protein Roq1 / NAD(+) hydrolase RPV1 / Recognition of XopQ 1 protein


Mass: 150648.391 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana benthamiana (plant) / Gene: ROQ1 / Production host: Nicotiana benthamiana (plant) / Tissue (production host): Leaves
References: UniProt: A0A290U7C4, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Roq1COMPLEX#10RECOMBINANT
2XopQCOMPLEX#11RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.150 MDaNO
210.049819 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Nicotiana benthamiana (plant)4100
32Xanthomonas euvesicatoria (bacteria)456327
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Nicotiana benthamiana (plant)4100
32Nicotiana benthamiana (plant)4100
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
110 mMHEPES1
21 mMEDTA1
35 mMMgCl21
4150 mMNaCl1
510 mMKCl1
63 %trehalose1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Sample was monodisperse.
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: 10 sec blot. Blot Force 10. 90 min incubation.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 80879 X / Nominal defocus max: -2500 nm / Nominal defocus min: -900 nm / Cs: 2.7 mm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 11134
Details: Images were collected as dose-fractionated movie frames.
EM imaging opticsEnergyfilter name: GIF Bioquantum

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.18_3845refinement
PHENIX1.18_3845refinement
EM software
IDNameVersionCategory
1RELION3.1particle selection
2SerialEMimage acquisition
4Gctf1.18CTF correction
7Cootmodel fitting
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D reconstruction
13PHENIX1.18model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1254987
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15263 / Num. of class averages: 1 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 38.64 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003214612
ELECTRON MICROSCOPYf_angle_d0.739519712
ELECTRON MICROSCOPYf_chiral_restr0.0482192
ELECTRON MICROSCOPYf_plane_restr0.00432464
ELECTRON MICROSCOPYf_dihedral_angle_d25.51395548
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AELECTRON MICROSCOPYNCS constraints0.000495896907796
ens_1d_3AELECTRON MICROSCOPYNCS constraints0.000506311474322
ens_1d_4AELECTRON MICROSCOPYNCS constraints0.000506133687496
ens_2d_2BELECTRON MICROSCOPYNCS constraints0.000495705704575
ens_2d_3BELECTRON MICROSCOPYNCS constraints0.000468016418624
ens_2d_4BELECTRON MICROSCOPYNCS constraints0.000480983188133

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