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 and replication of Pseudomonas aeruginosa phage JBD30.
Journal, issue, pages	EMBO J, Vol. 43, Issue 19, Page 4384-4405, Year 2024
Publish date	Aug 14, 2024
Authors	Lucie Valentová / Tibor Füzik / Jiří Nováček / Zuzana Hlavenková / Jakub Pospíšil / Pavel Plevka /
PubMed Abstract	Bacteriophages are the most abundant biological entities on Earth, but our understanding of many aspects of their lifecycles is still incomplete. Here, we have structurally analysed the infection ...Bacteriophages are the most abundant biological entities on Earth, but our understanding of many aspects of their lifecycles is still incomplete. Here, we have structurally analysed the infection cycle of the siphophage Casadabanvirus JBD30. Using its baseplate, JBD30 attaches to Pseudomonas aeruginosa via the bacterial type IV pilus, whose subsequent retraction brings the phage to the bacterial cell surface. Cryo-electron microscopy structures of the baseplate-pilus complex show that the tripod of baseplate receptor-binding proteins attaches to the outer bacterial membrane. The tripod and baseplate then open to release three copies of the tape-measure protein, an event that is followed by DNA ejection. JBD30 major capsid proteins assemble into procapsids, which expand by 7% in diameter upon filling with phage dsDNA. The DNA-filled heads are finally joined with 180-nm-long tails, which bend easily because flexible loops mediate contacts between the successive discs of major tail proteins. It is likely that the structural features and replication mechanisms described here are conserved among siphophages that utilize the type IV pili for initial cell attachment.
External links	EMBO J / PubMed:39143239 / PubMed Central
Methods	EM (single particle)
Resolution	2.57 - 26.0 Å
Structure data	19256 8rk3 EMDB-19256, PDB-8rk3: Bacteriophage JBD30 baseplate - composite structure Method: EM (single particle) / Resolution: 4.46 Å EMDB-19257: Bacteriophage JBD30 capsid - assymetric reconstruction Method: EM (single particle) / Resolution: 8.33 Å EMDB-19258: Bacteriophage JBD30 procapsid computed with C5 symmetry Method: EM (single particle) / Resolution: 6.92 Å 19259 8rk4 EMDB-19259, PDB-8rk4: Receptor binding protein of bacteriophage JBD30 computed with C3 symmetry Method: EM (single particle) / Resolution: 4.74 Å 19260 8rk5 EMDB-19260, PDB-8rk5: Tail fibres of bacteriophage JBD30 Method: EM (single particle) / Resolution: 4.54 Å EMDB-19261: Baseplate of bacteriophage JBD30 Method: EM (single particle) / Resolution: 9.0 Å 19262 8rk6 EMDB-19262, PDB-8rk6: Baseplate core of bacteriophage JBD30 computed in C3 symmetry Method: EM (single particle) / Resolution: 3.6 Å 19263 8rk7 EMDB-19263, PDB-8rk7: Baseplate of bacteriophage JBD30 computed in C3 symmetry Method: EM (single particle) / Resolution: 4.46 Å 19264 8rk8 EMDB-19264, PDB-8rk8: Tail of bacteriophage JBD30 computed in C6 symmetry Method: EM (single particle) / Resolution: 3.88 Å 19265 8rk9 EMDB-19265, PDB-8rk9: Stopper protein of bacteriophage JBD30 computed in C6 symmetry Method: EM (single particle) / Resolution: 3.95 Å 19266 8rka EMDB-19266, PDB-8rka: Connector complex of empty bacteriophage JBD30 particle computed in C12 symmetry Method: EM (single particle) / Resolution: 3.12 Å 19267 8rkb EMDB-19267, PDB-8rkb: Connector complex of bacteriophage JBD30 computed in C12 symmetry Method: EM (single particle) / Resolution: 3.12 Å EMDB-19268: Capsid-connector interface of bacteriophage JBD30 Method: EM (single particle) / Resolution: 7.61 Å EMDB-19269: Capsid of bacteriophage JBD30 decorated with minor capsid protein trimers - asymmetric reconstruction Method: EM (single particle) / Resolution: 18.59 Å 19270 8rkc EMDB-19270, PDB-8rkc: Capsid of bacteriophage JBD30 decorated with minor capsid protein trimers computed in I4 symmetry Method: EM (single particle) / Resolution: 2.95 Å EMDB-19271: Capsid of bacteriophage JBD30 decorated with minor capsid protein trimers computed in C5 symmetry Method: EM (single particle) / Resolution: 4.6 Å EMDB-19272: Capsid of bacteriophage JBD30 - asymmetric reconstruction Method: EM (single particle) / Resolution: 4.93 Å EMDB-19273: Capsid of empty bacteriophage JBD30 particle computed in C5 symmetry Method: EM (single particle) / Resolution: 3.52 Å EMDB-19274: Capsid of bacteriophage JBD30 computed in C5 symmetry Method: EM (single particle) / Resolution: 3.37 Å 19280 8rkn EMDB-19280, PDB-8rkn: Bacteriophage JBD30 capsid Method: EM (single particle) / Resolution: 2.57 Å 19281 8rko EMDB-19281, PDB-8rko: Bacteriophage JBD30 empty particle capsid Method: EM (single particle) / Resolution: 2.58 Å 19285 8rkx EMDB-19285, PDB-8rkx: Procapsid of bacteriophage JBD30 computed in I4 symmetry Method: EM (single particle) / Resolution: 4.01 Å 19439 8rqe EMDB-19439, PDB-8rqe: Composite map of bacteriophage JBD30 capsid - neck complex Method: EM (single particle) / Resolution: 8.0 Å EMDB-19561: Bacteriophage JBD30 baseplate bound to pili type IV Method: EM (single particle) / Resolution: 26.0 Å
Chemicals	ChemComp-FE: Unknown entry
Source	pseudomonas phage jbd30 (virus)
Keywords	VIRUS / bacteriophage JBD30 / virion / baseplate / bacteriophage / receptor binding protein / tail fibre / baseplate core / baseplate upper protein / distal tail protein / baseplate hub protein / baseplate hub / tail / major tail protein / VIRAL PROTEIN / connector / stopper / head completion protein 2 / connector complex / portal / adaptor / empty particle / portal protein / adaptor protein / capsid / minor capsid protein / major capsid protein / procapsid / neck