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- EMDB-38551: The map of chimeric RyR transmembrane domain in complex with flub... -

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Basic information

Entry
Database: EMDB / ID: EMD-38551
TitleThe map of chimeric RyR transmembrane domain in complex with flubendiamide after TMD local refinement
Map data
Sample
  • Complex: chimeric RyR1 Ca2+/ATP/caffeine/CaM1234/FLU
Keywordsryanodine receptor / FLU / ion channel / diamide insecticide / MEMBRANE PROTEIN
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.82 Å
AuthorsLin L / Wang C / Wang W / Jiang H / Van Petegem F / Yuchi Z
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32372580 China
National Natural Science Foundation of China (NSFC)32022073 China
Ministry of Science and Technology (MoST, China)2022YFE0108400 China
CitationJournal: Nat Commun / Year: 2024
Title: Cryo-EM structures of ryanodine receptors and diamide insecticides reveal the mechanisms of selectivity and resistance.
Authors: Lianyun Lin / Changshi Wang / Wenlan Wang / Heng Jiang / Takashi Murayama / Takuya Kobayashi / Hadiatullah Hadiatullah / Yu Seby Chen / Shunfan Wu / Yiwen Wang / Henryk Korza / Yucheng Gu / ...Authors: Lianyun Lin / Changshi Wang / Wenlan Wang / Heng Jiang / Takashi Murayama / Takuya Kobayashi / Hadiatullah Hadiatullah / Yu Seby Chen / Shunfan Wu / Yiwen Wang / Henryk Korza / Yucheng Gu / Yan Zhang / Jiamu Du / Filip Van Petegem / Zhiguang Yuchi /
Abstract: The resistance of pests to common insecticides is a global issue that threatens food production worldwide. Diamide insecticides target insect ryanodine receptors (RyRs), causing uncontrolled calcium ...The resistance of pests to common insecticides is a global issue that threatens food production worldwide. Diamide insecticides target insect ryanodine receptors (RyRs), causing uncontrolled calcium release from the sarcoplasmic and endoplasmic reticulum. Despite their high potency and species selectivity, several resistance mutations have emerged. Using a chimeric RyR (chiRyR) approach and cryo-electron microscopy (cryo-EM), we investigate how insect RyRs engage two different diamide insecticides from separate families: flubendiamide, a phthalic acid derivative, and tetraniliprole, an anthranilic compound. Both compounds target the same site in the transmembrane region of the RyR, albeit with different poses, and promote channel opening through coupling with the pore-forming domain. To explore the resistance mechanisms, we also solve two cryo-EM structures of chiRyR carrying the two most common resistance mutations, I4790M and G4946E, both alone and in complex with the diamide insecticide chlorantraniliprole. The resistance mutations perturb the local structure, directly reducing the binding affinity and altering the binding pose. Our findings elucidate the mode of action of different diamide insecticides, reveal the molecular mechanism of resistance mutations, and provide important clues for the development of novel pesticides that can bypass the resistance mutations.
History
DepositionJan 3, 2024-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38551.png

Downloads & links

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Map

FileDownload / File: emd_38551.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 512 pix.
= 542.72 Å		1.06 Å/pix.
x 512 pix.
= 542.72 Å		1.06 Å/pix.
x 512 pix.
= 542.72 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.2243486 - 0.36612272
Average (Standard dev.)-0.000060567978 (±0.010606491)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 542.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_38551_msk_1.map
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AxesZYX

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Half map: #1

Fileemd_38551_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_38551_half_map_2.map
Projections & Slices
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Sample components

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Entire : chimeric RyR1 Ca2+/ATP/caffeine/CaM1234/FLU

EntireName: chimeric RyR1 Ca2+/ATP/caffeine/CaM1234/FLU
Components
  • Complex: chimeric RyR1 Ca2+/ATP/caffeine/CaM1234/FLU

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Supramolecule #1: chimeric RyR1 Ca2+/ATP/caffeine/CaM1234/FLU

SupramoleculeName: chimeric RyR1 Ca2+/ATP/caffeine/CaM1234/FLU / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 2.54 MDa

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6m2w

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.82 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 42349
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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