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 infection dynamics of mycobacteriophage Bxb1.
Journal, issue, pages	Cell, Year 2025
Publish date	Apr 14, 2025
Authors	Krista G Freeman / Sudipta Mondal / Lourriel S Macale / Jennifer Podgorski / Simon J White / Benjamin H Silva / Valery Ortiz / Alexis Huet / Ronelito J Perez / Joemark T Narsico / Meng-Chiao Ho / Deborah Jacobs-Sera / Todd L Lowary / James F Conway / Donghyun Park / Graham F Hatfull /
PubMed Abstract	Mycobacteriophage Bxb1 is a well-characterized virus of Mycobacterium smegmatis with double-stranded DNA and a long, flexible tail. Mycobacteriophages show considerable potential as therapies for ...Mycobacteriophage Bxb1 is a well-characterized virus of Mycobacterium smegmatis with double-stranded DNA and a long, flexible tail. Mycobacteriophages show considerable potential as therapies for Mycobacterium infections, but little is known about the structural details of these phages or how they bind to and traverse the complex Mycobacterium cell wall. Here, we report the complete structure and atomic model of phage Bxb1, including the arrangement of immunodominant domains of both the capsid and tail tube subunits, as well as the assembly of the protein subunits in the tail-tip complex. The structure contains protein assemblies with 3-, 5-, 6-, and 12-fold symmetries, which interact to satisfy several symmetry mismatches. Cryoelectron tomography of phage particles bound to M. smegmatis reveals the structural transitions that occur for free phage particles to bind to the cell surface and navigate through the cell wall to enable DNA transfer into the cytoplasm.
External links	Cell / PubMed:40239650
Methods	EM (single particle) / EM (subtomogram averaging)
Resolution	2.45 - 26.0 Å
Structure data	EMDB-46656: Mycobacteriophage Bxb1 tail tip - Consensus C3 map Method: EM (single particle) / Resolution: 2.45 Å EMDB-46657: Mycobacteriophage Bxb1 tail tip - Tail spike C1 local refinement Method: EM (single particle) / Resolution: 2.85 Å EMDB-46658: Mycobacteriophage Bxb1 tail tip - Tail wings C1 local refinement Method: EM (single particle) / Resolution: 3.98 Å EMDB-46659: Mycobacteriophage Bxb1 tail tip - Tail collar and fibers C1 local refinement Method: EM (single particle) / Resolution: 3.65 Å 46661 9d93 EMDB-46661, PDB-9d93: Mycobacteriophage Bxb1 tail tip - Composite map and model Method: EM (single particle) / Resolution: 2.85 Å EMDB-46663: Mycobacteriophage Bxb1 portal and connector assembly - C3 consensus refinement Method: EM (single particle) / Resolution: 3.3 Å EMDB-46666: Mycobacteriophage Bxb1 portal and connector assembly - Portal and head-to-tail adaptor C12 local refinement Method: EM (single particle) / Resolution: 2.69 Å EMDB-46667: Mycobacteriophage Bxb1 portal and connector assembly - Head-to-tail stopper and tail terminator C6 local refinement Method: EM (single particle) / Resolution: 2.68 Å EMDB-46668: Mycobacteriophage Bxb1 portal and connector assembly - Tail tube C3 local refinement Method: EM (single particle) / Resolution: 3.06 Å 46669 9d94 EMDB-46669, PDB-9d94: Mycobacteriophage Bxb1 portal and connector assembly - Composite map and model Method: EM (single particle) / Resolution: 3.0 Å EMDB-46673: Mycobacteriophage Bxb1 tail tube segment - C1 consensus refinement Method: EM (single particle) / Resolution: 3.11 Å EMDB-46674: Mycobacteriophage Bxb1 tail tube segment - Core C1 local refinement Method: EM (single particle) / Resolution: 2.99 Å EMDB-46675: Mycobacteriophage Bxb1 tail tube segment - CTE domain C1 local refinement Method: EM (single particle) / Resolution: 4.88 Å 46676 9d9l EMDB-46676, PDB-9d9l: Mycobacteriophage Bxb1 tail tube segment - Composite map and model Method: EM (single particle) / Resolution: 4.0 Å EMDB-46678: Mycobacteriophage Bxb1 C1 Capsid and Portal - C1 consensus map Method: EM (single particle) / Resolution: 3.44 Å EMDB-46679: Mycobacteriophage Bxb1 C1 Capsid and Portal - Portal C1 local refinement Method: EM (single particle) / Resolution: 3.31 Å 46681 9d9w EMDB-46681, PDB-9d9w: Mycobacteriophage Bxb1 C1 Capsid and Portal - Composite map and model Method: EM (single particle) / Resolution: 3.5 Å EMDB-46682: Mycobacteriophage Bxb1 Capsid - Icosahedral Consensus Map Method: EM (single particle) / Resolution: 2.71 Å EMDB-46684: Mycobacteriophage Bxb1 Capsid - Penton C1 local refinement Method: EM (single particle) / Resolution: 3.17 Å 46685 9d9x EMDB-46685, PDB-9d9x: Mycobacteriophage Bxb1 Capsid - Composite map and model Method: EM (single particle) / Resolution: 3.0 Å EMDB-46687: Mycobacteriophage BaDAS-1 Icosahedral Map Method: EM (single particle) / Resolution: 2.67 Å EMDB-46702: Subtomogram averaging of Bxb1 phage capsid (DNA-filled) during the infection state Method: EM (subtomogram averaging) / Resolution: 11.65 Å EMDB-46703: Subtomogram averaging of Bxb1 phage tail tube (DNA-filled) during the infection state Method: EM (subtomogram averaging) / Resolution: 7.0 Å EMDB-46704: Subtomogram averaging of Bxb1 phage capsid (emptied) during the infection state Method: EM (subtomogram averaging) / Resolution: 12.5 Å EMDB-46705: Subtomogram averaging of Bxb1 phage tail tube (emptied) during the infection state Method: EM (subtomogram averaging) / Resolution: 22.0 Å EMDB-46706: Subtomogram averaging of Bxb1 phage portal (DNA-filled) during the infection state Method: EM (subtomogram averaging) / Resolution: 23.0 Å EMDB-46707: Subtomogram averaging of Bxb1 phage portal (emptied) during the infection state Method: EM (subtomogram averaging) / Resolution: 26.0 Å EMDB-46723: Subtomogram averaging of Bxb1 phage tail tip complex during the infection state Method: EM (subtomogram averaging) / Resolution: 15.0 Å EMDB-48066: Subtomogram averaging of Bxb1 phage tail tip (infection state) Method: EM (subtomogram averaging) / Resolution: 8.48 Å EMDB-48067: Subtomogram averaging of Bxb1 phage tail tip (infection state, extra density within cell wall) Method: EM (subtomogram averaging) / Resolution: 24.0 Å
Source	mycobacterium phage bxb1 (virus)
Keywords	VIRAL PROTEIN / Bacteriophage / tail tip / portal / tail tube / VIRUS / Mycobacteriophage Bxb1 / capsid