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- EMDB-53991: Cryo-EM structure of tomato NRC3-AVRcap1b complex -

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Basic information

Entry
Database: EMDB / ID: EMD-53991
TitleCryo-EM structure of tomato NRC3-AVRcap1b complex
Map dataunsharpened composite map
Sample
  • Complex: SlNRC3-AVRcap1b complex
    • Complex: SlNRC3
      • Protein or peptide: SlNRC3
    • Complex: AVRcap1b
      • Protein or peptide: RxLR effector protein PITG_16705
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsEffector / NLR / Plant Immunity / Resistosome / IMMUNE SYSTEM
Function / homology
Function and homology information


defense response to other organism / ADP binding / host cell cytoplasm / extracellular region / membrane
Similarity search - Function
: / Effector PexRD54, WY-domain / Virus X resistance protein-like, coiled-coil domain / Rx, N-terminal / Rx N-terminal domain / Disease resistance protein Winged helix domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain ...: / Effector PexRD54, WY-domain / Virus X resistance protein-like, coiled-coil domain / Rx, N-terminal / Rx N-terminal domain / Disease resistance protein Winged helix domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / : / Leucine-rich repeat region / Leucine-rich repeat domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Uncharacterized protein / RxLR effector protein PITG_16705
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato) / Phytophthora infestans (potato late blight agent)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSeager BA / Kamoun S / Madhuprakash J
Funding support United Kingdom, European Union, 3 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V002937/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/Y002997/1 United Kingdom
European Research Council (ERC)EP/Y032187/1European Union
CitationJournal: To Be Published
Title: Cryo-EM structure of tomato NRC3-AVRcap1b complex
Authors: Seager BA / Kamoun S / Madhuprakash J
History
DepositionJun 11, 2025-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53991.png

Downloads & links

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Map

FileDownload / File: emd_53991.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened composite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 331.2 Å		0.83 Å/pix.
x 400 pix.
= 331.2 Å		0.83 Å/pix.
x 400 pix.
= 331.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.083432965 - 0.20189397
Average (Standard dev.)0.00032234783 (±0.0046197535)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 331.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sharpened composite map

Fileemd_53991_additional_1.map
Annotationsharpened composite map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SlNRC3-AVRcap1b complex

EntireName: SlNRC3-AVRcap1b complex
Components
  • Complex: SlNRC3-AVRcap1b complex
    • Complex: SlNRC3
      • Protein or peptide: SlNRC3
    • Complex: AVRcap1b
      • Protein or peptide: RxLR effector protein PITG_16705
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: SlNRC3-AVRcap1b complex

SupramoleculeName: SlNRC3-AVRcap1b complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Solanum lycopersicum (tomato)

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Supramolecule #2: SlNRC3

SupramoleculeName: SlNRC3 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Solanum lycopersicum (tomato)

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Supramolecule #3: AVRcap1b

SupramoleculeName: AVRcap1b / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Phytophthora infestans (potato late blight agent)

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Macromolecule #1: SlNRC3

MacromoleculeName: SlNRC3 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 104.763977 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString: MADVAVKFEL ENETQLEIDN ADLILGIQGE VENLLTDLNY FNAFLKEAAK SRRENEVLKE LVKKIRKVVN DAEDSIDKFV VEAKRHDDK NKFAQWFHIT HVARAKGVAD EIKSIRERVK EIRDNDAYGL QAITLDDNFN RGDEERKAPV VEEDDVVGFD D EAKTVIDR ...String:
MADVAVKFEL ENETQLEIDN ADLILGIQGE VENLLTDLNY FNAFLKEAAK SRRENEVLKE LVKKIRKVVN DAEDSIDKFV VEAKRHDDK NKFAQWFHIT HVARAKGVAD EIKSIRERVK EIRDNDAYGL QAITLDDNFN RGDEERKAPV VEEDDVVGFD D EAKTVIDR LIGGSDYVEV VPVVGMPGLG KTTLAYKIYK DPKVEYEFFT RVWVYVSQTF KRREIFLNII SKFTRNTKQY DD TPEDDLA NEVKELLGKG GKYLIVLDDV WTMEAWDRIK IAFPNNGKRN RVLMTTRQSN VAKRCNDKPH DLKFLTKDES WEL LEKKVF HKEKCPPELE LPGISIAEKC MGLPLAIVVI AGALIGKGKT TREWELVAAS VGEHLINRDP ENCKKLVQMS YDRL PYDLK ACFLYCGAFP GGSQIPAKKL IRLWIAEGFI QYQGPLALED VAEDHLNDLV NRNLVMVTQR SCSGQIKTCR VHDML HEFC RHEAMMEENL FQEIKQGQER SFPGKQELAT YRRLCIQSLI PEFLSMKPSG EHVRSFLCVG SKKIDMPPNE IPSIPK AFP LLRVLDAESI KFSRFSREFF KLFHLRYIAL STDKIKTIPA DFGNLWNIQT LIVETQQATL DIKADIWNMT RLRHVCT NA SATLPSTKRP KSSKDNLVNR CLQTLSTIAP ECCTAEVFTR TPNLKKLGVR GKIDALLESS KDGSGSGLFS NIGKLGCL E YLKLVNDTRL SSKPLHLPPA YIFPQKLKKL SLVDTWFEWK DMSILGLLPE LEVLKLKENA FKGQSWEQED GGFPRLQVL WIERTDLTSW KASSGNFPRL KHLALISCDK LEELPAELAD VKNLQLIELQ SSSESAARSA RAILKRNQEK EQDGDKGTGF KLSIFPHDL GLSDYKDHDG DYKDHDLDAA AADYKDDDDK

UniProtKB: Uncharacterized protein

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Macromolecule #2: RxLR effector protein PITG_16705

MacromoleculeName: RxLR effector protein PITG_16705 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Phytophthora infestans (potato late blight agent)
Molecular weightTheoretical: 78.138352 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString: MAPSIVENIK ALVKSSAVTP AKLQQWLDER LEAGLVFKNM NLDEPNIFSL LHEPNFAKWV QYADDLSAKS SHKESSVIST LTSLHGDKV VYDTIQAAKL YPQLSELALK LEKDQIRFWI ATRKDPSVVF EALNLNWAGI SIFPKPEFSA WLKYVDDVNA R HPKEAPLS ...String:
MAPSIVENIK ALVKSSAVTP AKLQQWLDER LEAGLVFKNM NLDEPNIFSL LHEPNFAKWV QYADDLSAKS SHKESSVIST LTSLHGDKV VYDTIQAAKL YPQLSELALK LEKDQIRFWI ATRKDPSVVF EALNLNWAGI SIFPKPEFSA WLKYVDDVNA R HPKEAPLS IIPTLKQRFS RGDEAGTDVL LKLIANGKAT TEAKTVANKV ESALFDFWLN SRETPDKVMD AFKYGTTTQA FL GSPRWKE WERYLSAYNA RYPEKKATAI ETLTRKYGDA QLLDTLIGAS SKGETKTLAA KLQAQQFDRW MNLKESPLDV YNR LRSSYG DTAFFNEPQL NVWVSYMNVF VDKNPSKVDK MFLELGDTFG DMRLFRVLGE AKKFPNLEST ATKLQMEKAS TLFA SGKSP EGIFKVLALD NVGDDILSNT LFHKWLAYLQ KFNKEHPNNQ ESWFDMLRIS YQPFGVERII ETGRKNPLTR LMAEK VENA YHNYWLDIKM EPKTAFRSLH LDESGEKLLA DPKFNTWVQY LKTFNDRYPN EKTTVIDGLR DNSHDIALLR MFSAAK NDP STEKLATDLQ SALILKWQDA KKTPEELKRV FVGVPAADEM LDRYIKLLAV ASSTPYSYPY DVPDYAGYPY DVPDYAG LY PYDVPDYATR AAYPYDVPDY AGYPYDVPDY AGLYPYDVPD YA

UniProtKB: RxLR effector protein PITG_16705

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 3 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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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

Concentration0.3 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
50.0 mMTris
150.0 mMSaltNaCl
5.0 mMSaltMgCl2
5.0 %Glycerol
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 7555 / Average electron dose: 50.13 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
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: 3531889
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: OTHER / Software - Name: cryoSPARC (ver. 4.6.2) / Details: composite map / Number images used: 267047
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.6.2)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL
Output model

PDB-9ria:
Cryo-EM structure of tomato NRC3-AVRcap1b complex

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