7Q0N | pdb_00007q0n

Arbitrium receptor from Katmira phage

• PDB DOI: https://doi.org/10.2210/pdb7Q0N/pdb
• NAKB: 7Q0N

• Classification: DNA BINDING PROTEIN
• Organism(s): Bacillaceae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-10-15 Released: 2022-06-01 
• Deposition Author(s): Gallego del Sol, F., Marina, A.
• Funding Organization(s): Spanish National Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.249 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Insights into the mechanism of action of the arbitrium communication system in SPbeta phages.

Gallego Del Sol, F., Quiles-Puchalt, N., Brady, A., Penades, J.R., Marina, A.

(2022) Nat Commun 13: 3627-3627

• PubMed: 35750663 
• DOI: https://doi.org/10.1038/s41467-022-31144-3
• Primary Citation Related Structures: 
  6S7I, 6S7L, 7Q0N


• PubMed Abstract: 
  

  The arbitrium system is employed by phages of the SPbeta family to communicate with their progeny during infection to decide either to follow the lytic or the lysogenic cycle. The system is controlled by a peptide, AimP, that binds to the regulator AimR, inhibiting its DNA-binding activity and expression of aimX. Although the structure of AimR has been elucidated for phages SPβ and phi3T, there is still controversy regarding the molecular mechanism of AimR function, with two different proposed models for SPβ. In this study, we deepen our understanding of the system by solving the structure of an additional AimR that shows chimerical characteristics with the SPβ receptor. The crystal structures of this AimR (apo, AimP-bound and DNA-bound) together with in vitro and in vivo analyses confirm a mechanism of action by AimP-induced conformational restriction, shedding light on peptide specificity and cross regulation with relevant biological implications.

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Organizational Affiliation: 
• Instituto de Biomedicina de Valencia (IBV), CSIC and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain.
MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK.
Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK. [e-mail].
Instituto de Biomedicina de Valencia (IBV), CSIC and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 118.9 kDa 
• Atom Count: 8,310 
• Modeled Residue Count: 862 
• Deposited Residue Count: 862 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arbitrium receptor	A, B	386	Bacillaceae	Mutation(s): 0  Gene Names: aimR, Goe11_c00800
UniProt
Find proteins for A0ACD6BAF3 (Bacillus phage vB_BsuS-Goe11) Explore A0ACD6BAF3  Go to UniProtKB:  A0ACD6BAF3

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (45-MER)	C	45	Bacillaceae

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (45-MER)	D	45	Bacillaceae

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.249 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.719	α = 90
b = 39.866	β = 100.49
c = 143.015	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-01 
Deposition Author(s): Gallego del Sol, F., Marina, A.

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Funding Organization	Location	Grant Number
Spanish National Research Council	Spain	--

Revision History  

• Version 1.0: 2022-06-01
  Type: Initial release
  
• Version 1.1: 2022-07-06
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description