8XKH

Structure of chimeric RyR Complex with tetraniliprole


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.87 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Cryo-EM structures of ryanodine receptors and diamide insecticides reveal the mechanisms of selectivity and resistance.

Lin, L.Wang, C.Wang, W.Jiang, H.Murayama, T.Kobayashi, T.Hadiatullah, H.Chen, Y.S.Wu, S.Wang, Y.Korza, H.Gu, Y.Zhang, Y.Du, J.Van Petegem, F.Yuchi, Z.

(2024) Nat Commun 15: 9056-9056

  • DOI: https://doi.org/10.1038/s41467-024-53490-0
  • Primary Citation of Related Structures:  
    8XJI, 8XKH, 8XLF, 8XLH, 8Y40

  • PubMed 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 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.


  • Organizational Affiliation

    Tianjin Key Laboratory for Modern Drug Delivery and High-Efficiency, Frontiers Science Center for Synthetic Biology, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Calmodulin-1A [auth J],
C [auth I],
E [auth L],
G [auth K]
149Homo sapiensMutation(s): 4 
Gene Names: CALM1CALMCAMCAM1
UniProt & NIH Common Fund Data Resources
Find proteins for P0DP23 (Homo sapiens)
Explore P0DP23 
Go to UniProtKB:  P0DP23
PHAROS:  P0DP23
GTEx:  ENSG00000198668 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DP23
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase FKBP1BB [auth F],
D [auth E],
F [auth H],
H [auth G]
107Homo sapiensMutation(s): 0 
Gene Names: FKBP1BFKBP12.6FKBP1LFKBP9OTK4
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P68106 (Homo sapiens)
Explore P68106 
Go to UniProtKB:  P68106
PHAROS:  P68106
GTEx:  ENSG00000119782 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68106
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ryanodine receptor 1I [auth D],
J [auth A],
K [auth B],
L [auth C]
5,037Oryctolagus cuniculusMutation(s): 4 
Gene Names: RYR1
UniProt
Find proteins for P11716 (Oryctolagus cuniculus)
Explore P11716 
Go to UniProtKB:  P11716
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11716
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1LV1 (Subject of Investigation/LOI)
Query on A1LV1

Download Ideal Coordinates CCD File 
AA [auth B],
FA [auth C],
Q [auth D],
V [auth A]
tetraniliprole
C22 H16 Cl F3 N10 O2
KNDVJPKNBVIKML-UHFFFAOYSA-N
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
DA [auth C],
O [auth D],
T [auth A],
Y [auth B]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
CFF (Subject of Investigation/LOI)
Query on CFF

Download Ideal Coordinates CCD File 
EA [auth C],
P [auth D],
U [auth A],
Z [auth B]
CAFFEINE
C8 H10 N4 O2
RYYVLZVUVIJVGH-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
BA [auth C],
M [auth D],
R [auth A],
W [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
CA [auth C],
N [auth D],
S [auth A],
X [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.87 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32372580
National Natural Science Foundation of China (NSFC)China32022073
Ministry of Science and Technology (MoST, China)China2022YFE0108400

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-30
    Type: Initial release