6LT9

The crystal structure of diamondback moth ryanodine receptor SPRY1 domain

• PDB DOI: https://doi.org/10.2210/pdb6LT9/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Plutella xylostella
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-01-22 Released: 2021-01-27 
• Deposition Author(s): Zhou, Y., Lin, L., Yuchi, Z.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.216 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Literature

The crystal structure of diamondback moth ryanodine receptor SPRY1 domain

Nayak, B., Zhou, Y., Salauddin, N., Lin, L., You, M., You, S., Yuchi, Z.

To be published.

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.52 kDa 
• Atom Count: 2,992 
• Modelled Residue Count: 362 
• Deposited Residue Count: 390 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ryanodine receptor 1	A [auth F], B	195	Plutella xylostella	Mutation(s): 2
UniProt
Find proteins for G8EME3 (Plutella xylostella) Explore G8EME3  Go to UniProtKB:  G8EME3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	C [auth F], E [auth B], F [auth B], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA (Subject of Investigation/LOI)	D [auth F], H [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.216 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.893	α = 90
b = 64.893	β = 90
c = 95.767	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-01-27 
Deposition Author(s): Zhou, Y., Lin, L., Yuchi, Z.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2017YFD0201400
Ministry of Science and Technology (MoST, China)	China	2017YFD0201403

Revision History  

• Version 1.0: 2021-01-27
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description