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

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Basic information

Entry
Database: PDB / ID: 7jlu
TitleStructure of the activated Roq1 resistosome directly recognizing the pathogen effector XopQ
Components
  • Disease resistance protein Roq1
  • XopQ
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 / Inosine/uridine-preferring nucleoside hydrolase domain / Inosine-uridine preferring nucleoside hydrolase / Ribonucleoside hydrolase-like / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / TIR domain ...C-JID domain / C-JID domain / Inosine/uridine-preferring nucleoside hydrolase domain / Inosine-uridine preferring nucleoside hydrolase / Ribonucleoside hydrolase-like / 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 / XopQ
Similarity search - Component
Biological speciesNicotiana benthamiana (plant)
Xanthomonas euvesicatoria (bacteria)
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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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-22380
  • Imaged by UCSF Chimera
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Assembly

Deposited unit
A: Disease resistance protein Roq1
B: XopQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,7493
Polymers204,7092
Non-polymers401
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_5551

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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.: 1
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
#2: Protein XopQ


Mass: 51341.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas euvesicatoria (bacteria) / Gene: xopQ / Production host: Nicotiana benthamiana (plant) / References: UniProt: Q5QA88
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / 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#1-#20RECOMBINANT
2XopQCOMPLEX#21RECOMBINANT
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 / Details: Kept at 4 degrees Celsius.
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: 90 min incubation. 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
IDNameVersionCategory
1RELION3.1particle selection
2SerialEMimage acquisition
4Gctf1.18CTF correction
7UCSF Chimera1.14model fitting
8Cootmodel fitting
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
14PHENIX1.18model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1254987
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15263 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingSpace: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 64.67 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038780
ELECTRON MICROSCOPYf_angle_d0.77211905
ELECTRON MICROSCOPYf_chiral_restr0.04631350
ELECTRON MICROSCOPYf_plane_restr0.00411515
ELECTRON MICROSCOPYf_dihedral_angle_d24.25383272

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