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- PDB-9h2l: Cryo-EM structure of an octameric G10-resistosome from wheat -

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Basic information

Entry
Database: PDB / ID: 9h2l
TitleCryo-EM structure of an octameric G10-resistosome from wheat
ComponentsNB-ARC domain-containing protein
KeywordsPLANT PROTEIN / G10-NLR / Octamer / Resistance / LRR
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
ADENOSINE-5'-TRIPHOSPHATE / NB-ARC domain-containing protein
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.95 Å
AuthorsGuo, G.H. / Zhao, H. / Lukoyanova, N. / Selvaraj, M. / Jones, J.
Funding support United Kingdom, 1items
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. / ...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, J.D.G.
History
DepositionOct 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NB-ARC domain-containing protein
B: NB-ARC domain-containing protein
C: NB-ARC domain-containing protein
D: NB-ARC domain-containing protein
E: NB-ARC domain-containing protein
F: NB-ARC domain-containing protein
G: NB-ARC domain-containing protein
H: NB-ARC domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)865,66116
Polymers861,6038
Non-polymers4,0578
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, The pdb file contains 8 chains of monomers and all these together form the homo octamer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
NB-ARC domain-containing protein / WAI-D3


Mass: 107700.422 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: This is a wheat resistance protein in G10-clade. / Source: (gene. exp.) Triticum aestivum (bread wheat) / Strain: M3405 / Gene: CFC21_030936 / Plasmid: pICSL86977OD
Details (production host): Binary vector with nos:bar:nos selection cassette and P-CaMV35s:(lacZ):T-osc in backbone. Accepts a single CDS-level 0 module (AATG-GCTT) between P-35s and T-ocs.
Organ (production host): leaves / Production host: Nicotiana benthamiana (plant) / References: UniProt: A0A3B6DHR8
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationN

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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

ComponentName: Wheat auto immunity -3 Protein / Type: COMPLEX / Details: This is a resistance protein in the wheat plant / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.856 MDa / Experimental value: NO
Source (natural)Organism: Triticum aestivum (bread wheat) / Organ: Leaves / Tissue: leaf
Source (recombinant)Organism: Nicotiana benthamiana (plant)
Buffer solutionpH: 7.5
Details: 150mM Tris HCl pH 7.5 150mM NaCl 1mM EDTA 1mM MgCl2
Buffer componentConc.: 150 mM / Name: Sodium chloride / Formula: NaCl
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: this is a protein sample purified from plant cell extract after over expression in leaf tissues
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K
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

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1300 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.94 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7044
Details: One grid was imaged at areas with good ice and several images
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1RELION5particle selection
2EPU3.4image acquisition
4RELION4CTF correction
7Cootmodel fitting
9RELION5initial Euler assignment
12RELION53D reconstruction
13PHENIX1.21_5207:model refinement
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C8 (8 fold cyclic)
3D reconstructionResolution: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12203 / Algorithm: BACK PROJECTION
Details: The half-maps and resolution were obtained using RELION software
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: The atomic model was fitted flexibly using coot and refined using Phenix realspace refinement module
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00355864
ELECTRON MICROSCOPYf_angle_d0.51875640
ELECTRON MICROSCOPYf_dihedral_angle_d6.157600
ELECTRON MICROSCOPYf_chiral_restr0.048744
ELECTRON MICROSCOPYf_plane_restr0.0039520

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