8QJK

Structure of the cytoplasmic domain of csx23 from Vibrio cholera in complex with cyclic tetra-adenylate (cA4)

• PDB DOI: https://doi.org/10.2210/pdb8QJK/pdb
• NAKB: 8QJK

• Classification: GENE REGULATION
• Organism(s): Vibrio cholerae, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-09-13 Released: 2024-08-07 
• Deposition Author(s): McMahon, S.A., McQuarrie, S., Gloster, T.M., Gruschow, S., White, M.F.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.272 
• R-Value Work: 0.243 

Starting Model: in silico

Literature

A cyclic-nucleotide binding membrane protein provides CRISPR-mediated antiphage defence in Vibrio cholera

McMahon, S.A., McQuarrie, S., Gloster, T.M., White, M.F., Gruschow, S., Ackermann, K., Bode, B.E.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 11.78 kDa 
• Atom Count: 759 
• Modelled Residue Count: 86 
• Deposited Residue Count: 100 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
csx23	A	96	Vibrio cholerae	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
Cyclic tetraadenosine monophosphate (cA4)	B [auth C]	4	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACE	C [auth A], D [auth A]	ACETYL GROUP C2 H4 O IKHGUXGNUITLKF-UHFFFAOYSA-N
NA	E [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002431	B [auth C]	Cyclic tetraadenosine monophosphate (cA4)	Polycyclic / Antiviral

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.272 
• R-Value Work: 0.243 
• Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.425	α = 90
b = 66.425	β = 90
c = 42.479	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-07 
Deposition Author(s): McMahon, S.A., McQuarrie, S., Gloster, T.M., Gruschow, S., White, M.F.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/T004789/1

Revision History  

• Version 1.0: 2024-08-07
  Type: Initial release