6M2W | pdb_00006m2w

Structure of RyR1 (Ca2+/Caffeine/ATP/CaM1234/CHL)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6M2W

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: 2,277.71 kDa 
  • Atom Count: 120,452 
  • Modeled Residue Count: 16,780 
  • Deposited Residue Count: 21,172 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ryanodine receptor 1,Ryanodine receptor 1,Ryanodine receptor 1,Ryanodine receptor 1,Ryanodine receptor 1,Ryanodine receptor 1,Ryanodine receptor 1
A, D, G, J
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, E, H, K
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:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Calmodulin-1
C, F, I, L
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

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP

Query on ATP



Download:Ideal Coordinates CCD File
DA [auth J],
O [auth A],
T [auth D],
Y [auth G]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
F0U
(Subject of Investigation/LOI)

Query on F0U



Download:Ideal Coordinates CCD File
AA [auth G],
FA [auth J],
Q [auth A],
V [auth D]
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
CFF

Query on CFF



Download:Ideal Coordinates CCD File
BA [auth J],
M [auth A],
R [auth D],
W [auth G]
CAFFEINE
C8 H10 N4 O2
RYYVLZVUVIJVGH-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
EA [auth J],
P [auth A],
U [auth D],
Z [auth G]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
CA [auth J],
N [auth A],
S [auth D],
X [auth G]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 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