6J6P

Crystal structure of diamondback moth ryanodine receptor phosphorylation domain(2836-3050) mutant S2946D

• PDB DOI: https://doi.org/10.2210/pdb6J6P/pdb

• Classification: METAL TRANSPORT
• Organism(s): Plutella xylostella
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-01-15 Released: 2019-09-04 
• Deposition Author(s): Xu, T., Lin, L., Yuchi, Z.
• Funding Organization(s): Ministry of Science and Technology (China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 0.225 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 

Literature

Crystal structure of diamondback moth ryanodine receptor Repeat34 domain reveals insect-specific phosphorylation sites.

Xu, T., Yuchi, Z.

(2019) BMC Biol 17: 77-77

• PubMed: 31597572 
• DOI: https://doi.org/10.1186/s12915-019-0698-5
• Primary Citation of Related Structures:  
  6J6O, 6J6P


• PubMed Abstract: 
  

  Ryanodine receptor (RyR), a calcium-release channel located in the sarcoplasmic reticulum membrane of muscles, is the target of insecticides used against a wide range of agricultural pests. Mammalian RyRs have been shown to be under the regulatory control of several kinases and phosphatases, but little is known about the regulation of insect RyRs by phosphorylation.

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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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 26.28 kDa 
• Atom Count: 1,851 
• Modelled Residue Count: 192 
• Deposited Residue Count: 218 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ryanodine receptor	A	218	Plutella xylostella	Mutation(s): 4  Gene Names: RyR
UniProt
Find proteins for I3NWV8 (Plutella xylostella) Explore I3NWV8  Go to UniProtKB:  I3NWV8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	B [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
GOL	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 0.225 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.828	α = 90
b = 55.828	β = 90
c = 131.552	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-04 
Deposition Author(s): Xu, T., Lin, L., Yuchi, Z.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (China)	China	--

Revision History  

• Version 1.0: 2019-09-04
  Type: Initial release
  
• Version 1.1: 2019-10-16
  Changes: Data collection, Database references
• Version 1.2: 2019-10-23
  Changes: Data collection, Database references
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Refinement description