9SF2 | pdb_00009sf2

Phage Phi106 repressor in complex with AimX

PDB DOI: https://doi.org/10.2210/pdb9SF2/pdb

Classification: VIRAL PROTEIN
Organism(s): Bacillaceae bacterium
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-08-19 Released: 2026-01-14
Deposition Author(s): Marina, A., Martinez Alonso, C., Gallego del Sol, F.
Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.219 (Depositor), 0.219 (DCC)
R-Value Work:
0.179 (Depositor), 0.179 (DCC)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

A widespread extended arbitrium system controls lysis/lysogeny through antirepression.

Kabel, S., Omer Bendori, S., Borenstein, T., Guler, P., Martinez-Alonso, C., Mancheno-Bonillo, J., Gallego-Del-Sol, F., Marina, A., Eldar, A.

(2026) Cell Host Microbe 34: 278

PubMed: 41619737 Search on PubMed
DOI: https://doi.org/10.1016/j.chom.2026.01.007
Primary Citation of Related Structures:
9IAQ, 9SF2

PubMed Abstract:
Many temperate Bacillus phages use the arbitrium peptide-based signaling system to regulate lysis-lysogeny decisions. In this system, the secreted AimP peptide inhibits the AimR receptor to promote lysogeny. However, the downstream mechanism of AimR-mediated lysis control remains unclear for most systems. Here, we identify that ∼75% of arbitrium systems possess an extended five-gene module, including the aimX, aimC, and aimL genes. AimX encodes a small AimR-regulated antirepressor protein that binds the phage repressor AimC, preventing its oligomerization and DNA binding, thereby activating the pro-lytic aimL gene and additional lytic genes. This mechanism was validated across multiple phages and structurally characterized, revealing that AimX mimics the AimC oligomerization domain to prevent oligomerization and inhibit repressor function. These findings elucidate the predominant molecular strategy by which arbitrium systems control phage lysis-lysogeny transitions and highlight the central role of small proteins in phage decision-making.

Organizational Affiliation

Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel Aviv University, 6139001 Tel Aviv, Israel.

Macromolecule Content

Total Structure Weight: 18.99 kDa
Atom Count: 1,353
Modeled Residue Count: 151
Deposited Residue Count: 158
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator	A	129	Bacillaceae bacterium	Mutation(s): 0 Gene Names: BSI_13000
UniProt
Find proteins for A0A9W5PE21 (Bacillus inaquosorum KCTC 13429) Explore A0A9W5PE21 Go to UniProtKB: A0A9W5PE21
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A9W5PE21
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacillus phage phi106 antirepressor	B	29	Bacillaceae bacterium	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A], H [auth B], I [auth B], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] K [auth B] L [auth B] D [auth A], E [auth A], F [auth A], K [auth B], L [auth B], M [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]