7CF9 | pdb_00007cf9

Structure of RyR1 (Ca2+/CHL)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7CF9

This is version 1.2 of the entry. See complete history

Literature

Structural basis for diamide modulation of ryanodine receptor.

Ma, R.Haji-Ghassemi, O.Ma, D.Jiang, H.Lin, L.Yao, L.Samurkas, A.Li, Y.Wang, Y.Cao, P.Wu, S.Zhang, Y.Murayama, T.Moussian, B.Van Petegem, F.Yuchi, Z.

(2020) Nat Chem Biol 16: 1246-1254

  • DOI: https://doi.org/10.1038/s41589-020-0627-5
  • Primary Citation Related Structures: 
    6M2W, 7CF9

  • PubMed Abstract: 

    The diamide insecticide class is one of the top-selling insecticides globally. They are used to control a wide range of pests by targeting their ryanodine receptors (RyRs). Here, we report the highest-resolution cryo-electron microscopy (cryo-EM) structure of RyR1 in the open state, in complex with the anthranilic diamide chlorantraniliprole (CHL). The 3.2-Å local resolution map facilitates unambiguous assignment of the CHL binding site. The molecule induces a conformational change by affecting the S4-S5 linker, triggering channel opening. The binding site is further corroborated by mutagenesis data, which reveal how diamide insecticides are selective to the Lepidoptera group of insects over honeybee or mammalian RyRs. Our data reveal that several pests have developed resistance via two mechanisms, steric hindrance and loss of contact. Our results provide a foundation for the development of highly selective pesticides aimed at overcoming resistance and therapeutic molecules to treat human myopathies.


  • Organizational Affiliation
    • Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China.

Macromolecule Content 

  • Total Structure Weight: 2,208.37 kDa 
  • Atom Count: 116,104 
  • Modeled Residue Count: 16,224 
  • Deposited Residue Count: 20,576 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ryanodine receptor 1,RyR1
A, C, E, G
5,037Oryctolagus cuniculusMutation(s): 0 
Membrane Entity: Yes 
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
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase FKBP1B
B, D, F, H
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

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F0U
(Subject of Investigation/LOI)

Query on F0U



Download:Ideal Coordinates CCD File
K [auth A],
N [auth C],
Q [auth E],
T [auth G]
5-bromanyl-N-[4-chloranyl-2-methyl-6-(methylcarbamoyl)phenyl]-2-(3-chloranylpyridin-2-yl)pyrazole-3-carboxamide
C18 H14 Br Cl2 N5 O2
PSOVNZZNOMJUBI-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
J [auth A],
M [auth C],
P [auth E],
S [auth G]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
I [auth A],
L [auth C],
O [auth E],
R [auth G]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.70 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)China31972287
Ministry of Science and Technology (MoST, China)China2017YFD0201400
Ministry of Science and Technology (MoST, China)China2017YFD0201403
Canadian Institutes of Health Research (CIHR)CanadaPJT-159601

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-02
    Type: Initial release
  • Version 1.1: 2020-10-28
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references