Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structure of defense against restriction proteins DarA and Hdf in phage P1 reveals a new molecular mechanism during phage assembly, infection and DNA ejection.
Journal, issue, pages	PLoS Pathog, Vol. 22, Issue 1, Page e1013869, Year 2026
Publish date	Jan 16, 2026
Authors	Jing Zheng / Yuan Chen / Siting Chen / Junquan Zhou / Hao Xiao / Fan Yang / Hongrong Liu /
PubMed Abstract	The continuous "arms race" between bacterial antiviral defense systems and phage anti-defense strategies drives evolutionary innovation. Previous study indicated that the defense against restriction ...The continuous "arms race" between bacterial antiviral defense systems and phage anti-defense strategies drives evolutionary innovation. Previous study indicated that the defense against restriction (Dar) proteins DarA and Hdf in myophage P1 are associated with the head morphogenesis. However, the structural information for these proteins was lacking, and the mechanisms by which they mediate head morphogenesis and protect phage DNA against bacterial defense systems remained poorly understood. Using cryo-electron microscopy (cryo-EM), we resolved the entire structures of extended P1 and contracted P1 with partial DNA, with the latter lacking the baseplate, as well as the head structure of contracted P1 without DNA. We identified the structural proteins for the P1, including the head, connector complex, and baseplate, which exhibited conserved properties among the majority of myophages with a simple baseplate. Notably, 55 DarA-Hdf pairs are attached to the inner surface of head at each penton-hexon junction in the extended P1 and contracted P1 with partial DNA. The DarA and Hdf together form a complex that is tightly bound to the capsid and interacts with the DNA. However, these pairs are absent in the contracted P1 without DNA. Based on our three states of P1, we hypothesis that these extensive interactions among DarA, Hdf, DNA, and head play crucial roles in mediating capsid assembly, enhancing capsid stability, and protecting phage DNA. Our results provide a structural basis for further exploration of the mechanism by which Dar proteins function during phage assembly, infection and DNA ejection. This molecular mechanism may be conserved among P1-like phages.
External links	PLoS Pathog / PubMed:41544131 / PubMed Central
Methods	EM (single particle)
Resolution	3.2 - 7.3 Å
Structure data	64249 9ukm EMDB-64249, PDB-9ukm: Cryo-EM structure of bacteriophage P1 head Method: EM (single particle) / Resolution: 3.6 Å 64293 9ums EMDB-64293, PDB-9ums: Cryo-EM structure of bacteriophage P1 connector Method: EM (single particle) / Resolution: 3.5 Å 65154 9vl4 EMDB-65154, PDB-9vl4: Cryo-EM structure of bacteriophage P1 head at three-fold axis Method: EM (single particle) / Resolution: 3.6 Å EMDB-65450: Cryo-EM structure of the connector of contracted P1 Method: EM (single particle) / Resolution: 4.5 Å 65454 9vyi EMDB-65454, PDB-9vyi: Cryo-EM structure of bacteriophage P1 baseplate in C1 Method: EM (single particle) / Resolution: 3.7 Å 65475 9vz0 EMDB-65475, PDB-9vz0: Cryo-EM structure of the head of contracted P1 Method: EM (single particle) / Resolution: 4.0 Å 65480 9vzk EMDB-65480, PDB-9vzk: Cryo-EM structure of bacteriophage P1 baseplate in C3 Method: EM (single particle) / Resolution: 3.2 Å EMDB-65496: Cryo-EM structure of the head of phage P1 in the released state Method: EM (single particle) / Resolution: 7.3 Å
Source	escherichia phage p1 (virus)
Keywords	VIRAL PROTEIN / head / phage / connector / phag / baseplate / contracted phage P1