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

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Basic information

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


ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / ADP binding / defense response / signal transduction
Similarity search - Function
C-JID domain / C-JID 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 ...C-JID domain / C-JID 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
Disease resistance protein Roq1
Similarity search - Component
Biological speciesNicotiana benthamiana (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 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
B: Disease resistance protein Roq1
C: Disease resistance protein Roq1
A: Disease resistance protein Roq1
D: Disease resistance protein Roq1


Theoretical massNumber of molelcules
Total (without water)613,4684
Polymers613,4684
Non-polymers00
Water0
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 "B"
d_2ens_1chain "A"
d_1ens_2chain "C"
d_2ens_2chain "D"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERPHEA1 - 166
d_21ens_1SERPHEC1 - 166
d_11ens_2SERPHEB1 - 166
d_21ens_2SERPHED1 - 166

NCS ensembles :
ID
ens_1
ens_2

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Components

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


Mass: 153367.109 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)
References: UniProt: A0A290U7C4, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase

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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
1Roq1COMPLEXall0RECOMBINANT
2XopQCOMPLEX1RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.150 MDaNO
210.05 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 mMEDTAEthylenediaminetetraacetic acid1
35 mMMgCl21
4150 mMNaClSodium chloride1
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.

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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 FIELDBright-field microscopy / 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
IDNameVersionCategoryDetails
2SerialEMimage acquisition
4RELION3.1CTF correctionGCTF (v1.18)
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: C1 (asymmetric)
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5466 / Num. of class averages: 1 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 194.37 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00133284
ELECTRON MICROSCOPYf_angle_d0.34154572
ELECTRON MICROSCOPYf_chiral_restr0.0428632
ELECTRON MICROSCOPYf_plane_restr0.0014660
ELECTRON MICROSCOPYf_dihedral_angle_d3.8038660
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AELECTRON MICROSCOPYNCS constraints0.000717389023339
ens_2d_2BELECTRON MICROSCOPYNCS constraints0.000703936331411

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