6LQK | pdb_00006lqk

Crystal structure of honeybee RyR NTD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.288 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the N-terminal domain of ryanodine receptor from the honeybee, Apis mellifera.

Zhou, Y.Wang, W.Salauddin, N.M.Lin, L.You, M.You, S.Yuchi, Z.

(2020) Insect Biochem Mol Biol 125: 103454-103454

  • DOI: https://doi.org/10.1016/j.ibmb.2020.103454
  • Primary Citation Related Structures: 
    6LQK

  • PubMed Abstract: 

    Ryanodine receptors (RyRs) are the molecular target of diamides, a new chemical class of insecticides. Diamide insecticides are used to control lepidopteran pests and were considered relatively safe for mammals and non-targeted beneficial insects, including honey bees. However, recent studies showed that exposure to diamides could cause long-lasting locomotor deficits of bees. Here we report the crystal structure of RyR N-terminal domain A (NTD-A) from the honeybee, Apis mellifera, at 2.5 Å resolution. It shows a similar overall fold as the RyR NTD-A from mammals and the diamondback moth (DBM), Plutella xylostella, and still several loops located at the inter-domain interfaces show insect-specific or bee-specific structural features. A potential insecticide-binding pocket formed by loop9 and loop13 is conserved in lepidopteran but different in both mammals and bees, making it a good candidate targeting site for the development of pest-selective insecticides. Furthermore, a conserved intra-domain disulfide bond was observed in both DBM and bee RyR NTD-A crystal structures, which explains their higher thermal stability compared to mammalian RyR NTD-A. This work provides a basis for the development of novel insecticides with better selectivity between pests and bees by targeting a distinct site on pest RyRs, which would be a promising strategy to overcome the current toxicity problem.


  • 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, 300072, China; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China; Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002, China.

Macromolecule Content 

  • Total Structure Weight: 44.4 kDa 
  • Atom Count: 2,433 
  • Modeled Residue Count: 338 
  • Deposited Residue Count: 408 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ryanodine receptor
A, B
204Apis melliferaMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.288 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.054α = 90
b = 75.363β = 90
c = 143.878γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31972287
National Natural Science Foundation of China (NSFC)China31972271

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-20
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Structure summary