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	Ejectosome of bacteriophage ΦM1.
Journal, issue, pages	PNAS Nexus, Vol. 3, Issue 9, Page pgae416, Year 2024
Publish date	Sep 19, 2024
Authors	Alice-Roza Eruera / James Hodgkinson-Bean / Georgia L Rutter / Francesca R Hills / Rosheny Kumaran / Alexander J M Crowe / Nickhil Jadav / Fangfang Chang / Klemens McJarrow-Keller / Fátima Jorge / Jaekyung Hyun / Hyejin Kim / Bumhan Ryu / Mihnea Bostina /
PubMed Abstract	Podophages that infect gram-negative bacteria, such as pathogen ΦM1, encode tail assemblies too short to extend across the complex gram-negative cell wall. To overcome this, podophages encode a ...Podophages that infect gram-negative bacteria, such as pathogen ΦM1, encode tail assemblies too short to extend across the complex gram-negative cell wall. To overcome this, podophages encode a large protein complex (ejectosome) packaged inside the viral capsid and correspondingly ejected during infection to form a transient channel that spans the periplasmic space. Here, we describe the ejectosome of bacteriophage ΦM1 to a resolution of 3.32 Å by single-particle cryo-electron microscopy (cryo-EM). The core consists of tetrameric and octameric ejection proteins which form a ∼1.5-MDa ejectosome that must transition through the ∼30 Å aperture created by the short tail nozzle assembly that acts as the conduit for the passage of DNA during infection. The ejectosome forms several grooves into which coils of genomic DNA are fit before the DNA sharply turns and goes down the tunnel and into the portal. In addition, we reconstructed the icosahedral capsid and hybrid tail apparatus to resolutions between 3.04 and 3.23 Å, and note an uncommon fold adopted by the dimerized decoration proteins which further emphasize the structural diversity of podophages. These reconstructions have allowed the generation of a complete atomic model of the ΦM1, uncovering two distinct decoration proteins and highlighting the exquisite structural diversity of tailed bacteriophages.
External links	PNAS Nexus / PubMed:39351541 / PubMed Central
Methods	EM (single particle)
Resolution	2.98 - 10.32 Å
Structure data	43109 8vb0 EMDB-43109, PDB-8vb0: Asymmetric unit of bacteriophage PhiM1 mature capsid Method: EM (single particle) / Resolution: 3.04 Å 43110 8vb2 EMDB-43110, PDB-8vb2: C4 pre-infection ejectosome of the mature bacteriophage PhiM1 particle Method: EM (single particle) / Resolution: 3.32 Å EMDB-43111: Pectobacterium phage PhiM1 ejectosome C8 map Method: EM (single particle) / Resolution: 3.17 Å 43112 8vb4 EMDB-43112, PDB-8vb4: C12 portal and adaptor complex of the mature bacteriophage PhiM1 particle Method: EM (single particle) / Resolution: 2.98 Å 43127 8vbx EMDB-43127, PDB-8vbx: C6 nozzle and fibre complex of the mature bacteriophage PhiM1 particle Method: EM (single particle) / Resolution: 3.23 Å EMDB-43132: Asymmetric composite map of Pectobacterium phage PhiM1 Method: EM (single particle) / Resolution: 6.29 Å EMDB-43135: Pectobacterium phage PhiM1 D12 capsid dimer map Method: EM (single particle) / Resolution: 10.32 Å EMDB-46790: Asymmetric reconstruction of the PhiM1 tail and ejectosome complexes. Method: EM (single particle) / Resolution: 4.97 Å
Source	pectobacterium phage phim1 (virus)
Keywords	VIRUS / Mature capsid / Bacteriophage / Decoration protein / alpha-claw / VIRAL PROTEIN / ejectosome / internal core / internal proteins / core / mature phage / portal / phage / phage portal / portal complex / adaptor protein / portal adaptor complex / podophage / autographiviridae / Tail / fiber / fibre / complex / nozzle / protein / assembly