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- EMDB-46684: Mycobacteriophage Bxb1 Capsid - Penton C1 local refinement -

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Entry
Database: EMDB / ID: EMD-46684
TitleMycobacteriophage Bxb1 Capsid - Penton C1 local refinement
Map dataMycobacteriophage Bxb1 Capsid - Penton C1 local refinement
Sample
  • Virus: Mycobacterium phage Bxb1 (virus)
KeywordsBacteriophage / Mycobacteriophage Bxb1 / capsid / VIRUS
Biological speciesMycobacterium phage Bxb1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsFreeman KG
Funding support United States, Taiwan, 8 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)K99AI173544 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116884 United States
Howard Hughes Medical Institute (HHMI)GT12053 United States
National Institutes of Health/Office of the DirectorS10 OD025009 United States
National Institutes of Health/Office of the DirectorS10 OD019995 United States
National Institutes of Health/Office of the DirectorS10OD032467 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129547 United States
Academia Sinica (Taiwan)AS-IDR-110-06 Taiwan
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 21, 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_46684.png

Downloads & links

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Map

FileDownload / File: emd_46684.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMycobacteriophage Bxb1 Capsid - Penton C1 local refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 800 pix.
= 1056. Å		1.32 Å/pix.
x 800 pix.
= 1056. Å		1.32 Å/pix.
x 800 pix.
= 1056. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-0.9511415 - 2.1701844
Average (Standard dev.)-0.0054797255 (±0.1053045)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 1056.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_46684_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_46684_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_46684_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 : Mycobacterium phage Bxb1

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

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Supramolecule #1: Mycobacterium phage Bxb1

SupramoleculeName: Mycobacterium phage Bxb1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Portal and connector complex of Bxb1, containing five protein subunit types. This is a composite map, and related entries for consensus and locally refined maps are noted.
NCBI-ID: 2902907 / Sci species name: Mycobacterium phage Bxb1 / Sci species strain: Mycobacterium phage Bxb1 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration10 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMC4H11NO3Tris
1.0 mMMgSO4Magnesium sulfate
68.44 mMNaClSodium chloride
1.0 mMCaCl2Calcium chloride
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 268083
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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