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- EMDB-53429: Cryo-EM structure of plant resistance protein NRC2 dimer bound to... -

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Basic information

Entry
Database: EMDB / ID: EMD-53429
TitleCryo-EM structure of plant resistance protein NRC2 dimer bound to nematode effector SPRYSEC-15
Map data
Sample
  • Complex: Dimer of NRC2 bound with SS15 effector
    • Protein or peptide: NRC2a
  • Protein or peptide: Truncated secreted SPRY domain-containing protein 15
KeywordsHelper resistance protein / Plant immunity / Suppressor / PLANT PROTEIN
Function / homology
Function and homology information


defense response to other organism / ADP binding / defense response to virus / ATP binding
Similarity search - Function
Ran-binding protein Vid30/RanBPM/SPLA, SPRY 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 ...Ran-binding protein Vid30/RanBPM/SPLA, SPRY 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 / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Leucine-rich repeat domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Truncated secreted SPRY domain-containing protein 15 / NRC2a
Similarity search - Component
Biological speciesNicotiana benthamiana (plant) / Globodera rostochiensis (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsSelvaraj M / Kamoun S / Contreras M
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Gatsby Charitable Foundation United Kingdom
CitationJournal: To Be Published
Title: Cryo-EM structure of plant resistance protein NRC2 dimer bound to nematode effector SPRYSEC-15 (SS15)
Authors: Selvaraj M / Kamoun S / Contreras M
History
DepositionApr 15, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53429.png

Downloads & links

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Map

FileDownload / File: emd_53429.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.64 Å/pix.
x 400 pix.
= 256. Å		0.64 Å/pix.
x 400 pix.
= 256. Å		0.64 Å/pix.
x 400 pix.
= 256. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.64 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003
Minimum - Maximum-0.009851634 - 0.025845103
Average (Standard dev.)0.0000925194 (±0.00070439413)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 256.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53429_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_53429_additional_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53429_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53429_half_map_2.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 : Dimer of NRC2 bound with SS15 effector

EntireName: Dimer of NRC2 bound with SS15 effector
Components
  • Complex: Dimer of NRC2 bound with SS15 effector
    • Protein or peptide: NRC2a
  • Protein or peptide: Truncated secreted SPRY domain-containing protein 15

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Supramolecule #1: Dimer of NRC2 bound with SS15 effector

SupramoleculeName: Dimer of NRC2 bound with SS15 effector / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Nicotiana benthamiana (plant)
Molecular weightTheoretical: 250 KDa

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Macromolecule #1: NRC2a

MacromoleculeName: NRC2a / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Nicotiana benthamiana (plant)
Molecular weightTheoretical: 101.27 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString: MANVAVEFLV QNLMQLLRDN AELIVGVKDS AESLLQDLND FNAFLKQTAK SRTENDVHKE LVKKIKTVVN SAEDAIDKFV IEAKLHKDK GVGRFVDVKH YKRVYDVAGE IKTIRDKVKE IRLNNALDLQ ALQDEDQSAK GVQERKPPVV EEDDVVGFEE E ADKVINRL ...String:
MANVAVEFLV QNLMQLLRDN AELIVGVKDS AESLLQDLND FNAFLKQTAK SRTENDVHKE LVKKIKTVVN SAEDAIDKFV IEAKLHKDK GVGRFVDVKH YKRVYDVAGE IKTIRDKVKE IRLNNALDLQ ALQDEDQSAK GVQERKPPVV EEDDVVGFEE E ADKVINRL LGGSSGLEVV PVVGMPGLGK TTLANKIYKH PDIGYQFFTR IWVYVSQSYR RRELFLNIIS KFTRNTKQYH DM CEEDLAD EIEDFLGKGG KYLIVLDDVW SPDAWERIRI AFPNNNKSNR ILLTTRDSKV AKQCKQCIGI PHDLKFLTED ESW ILLEKK VFHKDKCPPE LELSGKSIAK KCNGLPLAIV VIAGALIGKG KTSREWKQVD ESVGEHLINK DQPENCNKLV QLSY DRLSY DLKACFLYCG AFPGGFEIPA WKLIRLWIAE GFIQYKGHLS LECKAEDNLN DLINRNLVMV MQRTSDGQIK TCRLH DMLH EFCRQEAMKE ENLFQEIKLG AEQYFPGKRE LATYRRLCIH SSVLEFISTK PSGEHVRSFL SFSLKKIEMP SVDIPT IPK GFPLLRVFDV ESINFSRFSK EFFQLYHLRY IAFSSDTIKI IPKHIGELWN IQTLIINTQQ RSLDIQANIW NMERLRH LH TNSSAKLPVP VTPRSSKVPL VNQSLQTLST IAPESCTEEV FARTPNLKKL GIRGKIAVLL EPNKSLLKNV KKLESLEN L KLINDSSQTG KGLRLPPSYI FPTKLRKLSL VDTWLEWNDM SILGQMEHLE VLKLKENGFM GECWESVGGF CSLLVLWIE RTDLVSWKAS ADHFPRLKHL VLICCDKLKE IPIGLADIRS FQVMELQNST KTAAISARGI RDKKDKQTQE GTNNNGFKLS IFPPDL

UniProtKB: NRC2a

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Macromolecule #2: Truncated secreted SPRY domain-containing protein 15

MacromoleculeName: Truncated secreted SPRY domain-containing protein 15 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Globodera rostochiensis (invertebrata)
Molecular weightTheoretical: 25.40224 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString: GPSPKANAKL EKVPSGNAES TPVLTLQNRW AYSARDEKLA WDSAARDEKL ELTEPAGLIV QFIGENSKHR SVRAKLPIPK GNSGIFYYE VTISGDGDAI YIGLATEQMP LRDTHVGYNE GTYGYGSSGK FWGHEVGGCS HWGNERPYID GQPKFDRNNI I GCGVNLKT ...String:
GPSPKANAKL EKVPSGNAES TPVLTLQNRW AYSARDEKLA WDSAARDEKL ELTEPAGLIV QFIGENSKHR SVRAKLPIPK GNSGIFYYE VTISGDGDAI YIGLATEQMP LRDTHVGYNE GTYGYGSSGK FWGHEVGGCS HWGNERPYID GQPKFDRNNI I GCGVNLKT RQIIYTHNGR PLETTGLLVA ESAAELYPCV SLFTSGNEIE ANFGTKPFKF NIAEGIDDVV GFEE

UniProtKB: Truncated secreted SPRY domain-containing protein 15

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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
Details: 150mM NaCl, 50mM Tris HCl (pH 7.5), 5mM DTT, 5% glycerol,
GridModel: Quantifoil Active R2/1 / Material: COPPER / Support film - Material: GRAPHENE / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV
Details0.3mg/ml

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 70.0 K
Specialist opticsPhase plate: OTHER / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 5174 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 27.0 µm / Nominal defocus min: 14.0 µm / Nominal magnification: 130000
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: 2044827
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 102500
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 3
FSC plot (resolution estimation)

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Atomic model buiding 1

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

PDB-9qww:
Cryo-EM structure of plant resistance protein NRC2 dimer bound to nematode effector SPRYSEC-15

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