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- EMDB-51852: Cryo-EM structure of an octameric G10-resistosome from wheat (N-t... -

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Basic information

Entry
Database: EMDB / ID: EMD-51852
TitleCryo-EM structure of an octameric G10-resistosome from wheat (N-to-N arrangement)
Map dataThis is final postprocessed EM map
Sample
  • Complex: Wheat auto immunity -3 Protein
    • Protein or peptide: NB-ARC domain-containing protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsG10-NLR / Octamer / Resistance / LRR / PLANT PROTEIN
Function / homology
Function and homology information


defense response / ADP binding
Similarity search - Function
: / Plant disease resistance protein RPS2-like, leucine-rich repeats / Disease resistance protein Winged helix domain / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. ...: / Plant disease resistance protein RPS2-like, leucine-rich repeats / Disease resistance protein Winged helix domain / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
NB-ARC domain-containing protein
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsGuo GH / Zhao H / Lukoyanova N / Selvaraj M / Jones J
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Gatsby Charitable Foundation United Kingdom
CitationJournal: Biorxiv / Year: 2025
Title: An activated wheat CCG10-NLR immune receptor forms an octameric resistosome
Authors: Guo G / Zhao H / Bai K / Wu Q / Dong L / Lu L / Chen Y / Hou Y / Lu J / Lu P / Li M / Zhang H / Wang G / Zhu K / Huang B / Cui X / Fu H / Hu C / Chu Z / Lyu X / Kamoun S / Wang C / Liu Z / Selvaraj M / Jones JDG
History
DepositionOct 19, 2024-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51852.png

Downloads & links

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Map

FileDownload / File: emd_51852.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is final postprocessed EM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 422.912 Å		0.83 Å/pix.
x 512 pix.
= 422.912 Å		0.83 Å/pix.
x 512 pix.
= 422.912 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0055
Minimum - Maximum-0.01680584 - 0.03726195
Average (Standard dev.)0.000157369 (±0.0015107341)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 422.912 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51852_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: This is halfmap 1

Fileemd_51852_half_map_1.map
AnnotationThis is halfmap 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_51852_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Wheat auto immunity -3 Protein

EntireName: Wheat auto immunity -3 Protein
Components
  • Complex: Wheat auto immunity -3 Protein
    • Protein or peptide: NB-ARC domain-containing protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Wheat auto immunity -3 Protein

SupramoleculeName: Wheat auto immunity -3 Protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: This is a resistance protein in the wheat plant in an N-to-N arrangement, where N-terminal domains connect two octamers
Source (natural)Organism: Triticum aestivum (bread wheat) / Organ: Leaves / Tissue: leaf
Molecular weightTheoretical: 1.712 MDa

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Macromolecule #1: NB-ARC domain-containing protein

MacromoleculeName: NB-ARC domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Triticum aestivum (bread wheat) / Strain: M3405
Molecular weightTheoretical: 107.700422 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString: MADAISAAGS CEQPECECLD GTGMLDAAAR EVASFLHLKS NWSDLDKAKK LLLAVETTVR ARVTAEVDKL NICDPQVQVW LRRVEELQL DAIDEDYSQL RKYSCLGQCT IHAHRRASIG RRVLEALDEA NKLIEEGRRF KKFGFKPLPK IVDPLPQIKT F GLETMLSQ ...String:
MADAISAAGS CEQPECECLD GTGMLDAAAR EVASFLHLKS NWSDLDKAKK LLLAVETTVR ARVTAEVDKL NICDPQVQVW LRRVEELQL DAIDEDYSQL RKYSCLGQCT IHAHRRASIG RRVLEALDEA NKLIEEGRRF KKFGFKPLPK IVDPLPQIKT F GLETMLSQ LYDLFEKGDS NIIGVWGQGG VGKTTLLHVF NNDLEKKAHD YQVVIFIEVS NSEALNTVEI QQTISERLNL PW NDAEPIA KRARFLIKAL GRKRFVILLD DVRKKFCLED VGIPTPDINS QSKLILTSRY REVCFQMNAQ RSLIEMQILG NDA SWELFL SKLSTETSAA VEPLGSQSAT REHAMKIAQS CGGLPLALNV IGTAVAGLEE GEWQSAADAI ATNMDNIDGV DEMF GRLKY SFDRLTPTQQ QCFLYCTLFP EYGSISKEQL IGYWLAEGLL LNDSEKGYQI IRSLVSACLL QVSGSMSSKV KMHHV IRQL GLWLVNKSDT KFLVQPGMAL DNAPSAEEWN EATRISIMSN NITELSFSPK CKNVTTLLMQ NNPNLNKMSY GFFRTM SSL KVLDLSHTAI TSLPECDALV ALEHLNLSHT HIMRLPERLW LLKELRHLDL SVTVAFEDTM NNCSKLHKLK VLNLFRS HY GIRDVDNLNL DSLKELLFLG ITIYAEDVLK KLNMPRPLAK STHRLNLKYC AEMQSIKISD LSHMEHLEEL YVESCYDL N TVVADAELTT SQLQFLTLSV LPSLESVLVA PMSHNFQYIR KLIISHCPKL SNITWVRRLQ LLERLVISHC DGVLEIVED EEQYGEQMKM QDHASYEQEE HAMVETSRND TGQSDFPKLR LIVLTGLKKL RSICKAREFP CLETLRVEDC PNLRSIPLSC THNYWKLKQ ICGSVEWWEK LQWENRKEVA CLDSKYFIPI GSDYKDHDGD YKDHDLDAAA ADYKDDDDK

UniProtKB: NB-ARC domain-containing protein

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 16 / 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

BufferpH: 7.5 / Component - Concentration: 150.0 mM / Component - Formula: NaCl / Component - Name: Sodium chloride
Details: 150mM Tris HCl pH 7.5 150mM NaCl 1mM EDTA 1mM MgCl2
GridModel: Quantifoil R1.2/1.3 / Support film - Material: GRAPHENE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: 3 microlitre of the sample was applied on a graphene coated Quantafoil grid R1.2/1.3 copper grid and vitrification was performed using vitrobot.
Detailsthis is a protein sample purified from plant cell extract after over expression in leaf tissues

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy 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: 7044 / Average exposure time: 1.94 sec. / Average electron dose: 50.0 e/Å2
Details: One grid was imaged at areas with good ice and several images
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 / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.3 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

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: OTHER / Details: ab-initio model reconstruction in relion
Final reconstructionApplied symmetry - Point group: D8 (2x8 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 13948
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsThe atomic model was fitted flexibly using coot and refined using Phenix realspace refinement module
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9h4i:
Cryo-EM structure of an octameric G10-resistosome from wheat (N-to-N arrangement)

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