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- EMDB-46707: Subtomogram averaging of Bxb1 phage portal (emptied) during the i... -

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Basic information

Entry
Database: EMDB / ID: EMD-46707
TitleSubtomogram averaging of Bxb1 phage portal (emptied) during the infection state
Map dataSubtomogram averaging of Bxb1 phage portal (emptied) during the infection state
Sample
  • Virus: Bxb1 (virus)
KeywordsPhage / tuberculosis / mycobacterium / VIRUS
Biological speciesBxb1 (virus)
Methodsubtomogram averaging / cryo EM / Resolution: 26.0 Å
AuthorsPark D / Mondal S
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Cell / Year: 2025
Title: Structure and infection dynamics of mycobacteriophage Bxb1.
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 ...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 /
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.
History
DepositionAug 23, 2024-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46707.png

Downloads & links

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Map

FileDownload / File: emd_46707.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram averaging of Bxb1 phage portal (emptied) during the infection state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 288 pix.
= 478.944 Å		1.66 Å/pix.
x 288 pix.
= 478.944 Å		1.66 Å/pix.
x 288 pix.
= 478.944 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.663 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2172.0
Minimum - Maximum0.0 - 4094.0
Average (Standard dev.)1838.257299999999987 (±220.932819999999992)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 478.944 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_46707_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_46707_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bxb1

EntireName: Bxb1 (virus)
Components
  • Virus: Bxb1 (virus)

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Supramolecule #1: Bxb1

SupramoleculeName: Bxb1 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 2902907 / Sci species name: Bxb1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 (ver. 99.58) / Number subtomograms used: 120
ExtractionNumber tomograms: 282 / Number images used: 120 / Software - Name: EMAN2 (ver. 2.99)
CTF correctionSoftware - Name: EMAN2 (ver. 99.58) / Type: PHASE FLIPPING ONLY
Final angle assignmentType: OTHER / Software - Name: EMAN2 (ver. 99.58)
FSC plot (resolution estimation)

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