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- EMDB-22381: Structure of the activated Roq1 resistosome directly recognizing ... -

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Basic information

Entry
Database: EMDB / ID: EMD-22381
TitleStructure of the activated Roq1 resistosome directly recognizing the pathogen effector XopQ
Map dataStructure of the activated Roq1 resistosome directly recognizing the pathogen effector XopQ
Sample
  • Complex: Roq1
    • Complex: XopQ
      • Protein or peptide: Disease resistance protein Roq1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsResistosome / Plant Immunity / Effector / LRR / TIR / NB-ARC / IMMUNE SYSTEM
Function / homology
Function and homology information


ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD+ nucleotidase, cyclic ADP-ribose generating / 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) / Xanthomonas euvesicatoria (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsMartin R / Qi T
Funding support United States, 1 items
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, 2020-
Header (metadata) releaseDec 2, 2020-
Map releaseDec 2, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7jlv
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7jlv
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22381.png

Downloads & links

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Map

FileDownload / File: emd_22381.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the activated Roq1 resistosome directly recognizing the pathogen effector XopQ
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 480 pix.
= 450.528 Å		0.94 Å/pix.
x 480 pix.
= 450.528 Å		0.94 Å/pix.
x 480 pix.
= 450.528 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9386 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.034604087 - 0.070845515
Average (Standard dev.)0.00000077 (±0.0024173171)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 450.528 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.93860.93860.9386
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z450.528450.528450.528
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.0350.0710.000

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Supplemental data

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Sample components

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Entire : Roq1

EntireName: Roq1
Components
  • Complex: Roq1
    • Complex: XopQ
      • Protein or peptide: Disease resistance protein Roq1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Roq1

SupramoleculeName: Roq1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Nicotiana benthamiana (plant)
Molecular weightTheoretical: 49.819 KDa

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Supramolecule #2: XopQ

SupramoleculeName: XopQ / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Xanthomonas euvesicatoria (bacteria)

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Macromolecule #1: Disease resistance protein Roq1

MacromoleculeName: Disease resistance protein Roq1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
Source (natural)Organism: Nicotiana benthamiana (plant)
Molecular weightTheoretical: 150.648391 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString: MLTSSSHHGR SYDVFLSFRG EDTRKTFVGH LFNALIEKGI HTFMDDKELK RGKSISSELM KAIGESRFAV VVFSKNYASS TWCLEELVK ILEIHEKFEL IVVPVFYDVD PSTVRKQNGE YAVCFTKFEA NLVDDRDKVL RWREALTKVA NISGHDLRNT Y NGDESKCI ...String:
MLTSSSHHGR SYDVFLSFRG EDTRKTFVGH LFNALIEKGI HTFMDDKELK RGKSISSELM KAIGESRFAV VVFSKNYASS TWCLEELVK ILEIHEKFEL IVVPVFYDVD PSTVRKQNGE YAVCFTKFEA NLVDDRDKVL RWREALTKVA NISGHDLRNT Y NGDESKCI QQILKDIFDK FCFSISITNR DLVGIESQIK KLSSLLRMDL KGVRLVGIWG MGGVGKTTAA RALFNRYYQN FE SACFLED VKEYLQHHTL LYLQKTLLSK LLKVEFVDCT DTEEMCVILK RRLCSKKVLV VLDDVNHNDQ LDKLVGAEDW FGS GSRIVI TTRDMKLLKN HDVHETYEIK VLEKDEAIEL FNLHAFKRSS PEKEFKELLN LVVDYTGGLP LALKVLGSLL YKED LDVWI STIDRLKDNP EGEIMATLKI SFDGLRDYEK SIFLDIACFF RGYNQRDMTA LFHASGFHPV LGVKTLVEKS LIFIL EDKI QMHDLMQEMG RQIAVQESPM RRIYRPEDVK DACIGDMRKE AIEGLLLTEP EQFEEGELEY MYSAEALKKT RRLRIL VKE YYNRGFDEPV AYLPNSLLWL EWRNYSSNSF PSNFEPSKLV YLTMKGSSII ELWNGAKRLA FLTTLDLSYC HKLIQTP DF RMITNLERLI LSSCDALVEV HPSVGFLKNL ILLNMDHCIS LERLPAIIQS ECLEVLDLNY CFNLKMFPEV ERNMTHLK K LDLTSTGIRE LPASIEHLSS LENLQMHSCN QLVSLPSSIW RFRNLKISEC EKLGSLPEIH GNSNCTRELI LKLVSIKEL PTSIGNLTSL NFLEICNCKT ISSLSSSIWG LTSLTTLKLL DCRKLKNLPG IPNAINHLSG HGLQLLLTLE QPTIYERLDL LRIIDMSWC SCISSLPHNI WMLKFLRILC ISYCSRLEYL PENLGHLEHL EELLADGTGI LRLPSSVARL NKLEVLSFRK K FAIGPKVQ YSSSMLNLPD DVFGSLGSLG SVVKLNLSGN GFCNLPETMN QLFCLEYLDI TFCQRLEALP ELPPSIKELY VD EHLALRI MEDLVIKCKE LNLIAVTKIE YQNFYRWLDS IWSDVSELLE NSQKQQLDDM LQLIPFSYLS TAKREEVLKI VIH GTRIPE WFRWQDRSAT TMSVNLPEYW YTENFLGFAI CCSCCFYHSA RSYDVEFEGS MHHYNYDSSY WKEYEEPSYD FYER DSIEI TAKLTPRHKG MRTEELKKVC SFSMNVLRRA TAVPNMCFAF FPFNSLCHIS NLQANNPNDY GIFETCLSPG DIRHR GKQW GFNLVYKDET GGSVTHEMLI NR

UniProtKB: Disease resistance protein Roq1

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationName
10.0 mMHEPES
1.0 mMEDTA
5.0 mMMgCl2
150.0 mMNaCl
10.0 mMKCl
3.0 %trehalose
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: 10 sec blot. Blot Force 10. 90 min incubation..
DetailsSample was monodisperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 11134 / Average electron dose: 50.0 e/Å2
Details: Images were collected as dose-fractionated movie frames.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 80879 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -2.5 µm / Nominal defocus min: -0.9 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1254987
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 15263
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 4 / Avg.num./class: 16613 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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