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- EMDB-46681: Mycobacteriophage Bxb1 C1 Capsid and Portal - Composite map and model -

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Basic information

Entry
Database: EMDB / ID: EMD-46681
TitleMycobacteriophage Bxb1 C1 Capsid and Portal - Composite map and model
Map dataMycobacteriophage Bxb1 C1 Capsid and Portal - Composite map and model
Sample
  • Virus: Mycobacterium phage Bxb1 (virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Portal protein
KeywordsBacteriophage / Mycobacteriophage Bxb1 / capsid / portal / VIRUS / VIRAL PROTEIN
Function / homologyPortal protein / Phage portal protein, SPP1 Gp6-like / : / Phage capsid / Phage capsid family / virion component / Major capsid protein / Portal protein
Function and homology information
Biological speciesMycobacterium phage Bxb1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsFreeman KG / White SJ / Huet A / Conway JF
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) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46681.png

Downloads & links

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Map

FileDownload / File: emd_46681.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMycobacteriophage Bxb1 C1 Capsid and Portal - Composite map and model
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 700 pix.
= 865.62 Å		1.24 Å/pix.
x 700 pix.
= 865.62 Å		1.24 Å/pix.
x 700 pix.
= 865.62 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2366 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.5
Minimum - Maximum-13.407826 - 32.850292000000003
Average (Standard dev.)0.008623685 (±1.0221128)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions700700700
Spacing700700700
CellA=B=C: 865.62006 Å
α=β=γ: 90.0 °

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Supplemental data

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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)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Portal protein

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Supramolecule #1: Mycobacterium phage Bxb1

SupramoleculeName: Mycobacterium phage Bxb1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
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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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 30 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium phage Bxb1 (virus)
Molecular weightTheoretical: 41.875461 KDa
SequenceString: MGFSADHSQI AQTKDTMFTG YLDPVQAKDY FAEAEKTSIV QRVAQKIPMG ATGIVIPHWT GDVSAQWIGE GDMKPITKGN MTKRDVHPA KIATIFVASA ETVRANPANY LGTMRTKVAT AIAMAFDNAA LHGTNAPSAF QGYLDQSNKT QSISPNAYQG L GVSGLTKL ...String:
MGFSADHSQI AQTKDTMFTG YLDPVQAKDY FAEAEKTSIV QRVAQKIPMG ATGIVIPHWT GDVSAQWIGE GDMKPITKGN MTKRDVHPA KIATIFVASA ETVRANPANY LGTMRTKVAT AIAMAFDNAA LHGTNAPSAF QGYLDQSNKT QSISPNAYQG L GVSGLTKL VTDGKKWTHT LLDDTVEPVL NGSVDANGRP LFVESTYESL TTPFREGRIL GRPTILSDHV AEGDVVGYAG DF SQIIWGQ VGGLSFDVTD QATLNLGSQE SPNFVSLWQH NLVAVRVEAE YGLLINDVNA FVKLTFDPVL TTYALDLDGA SAG NFTLSL DGKTSANIAY NASTATVKSA IVAIDDGVSA DDVTVTGSAG DYTITVPGTL TADFSGLTDG EGASISVVSV G

UniProtKB: Major capsid protein

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Macromolecule #2: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium phage Bxb1 (virus)
Molecular weightTheoretical: 53.822113 KDa
SequenceString: MAETESIDPE KLRDQLLDAF ENKQNELKSS KAYYDAERRP DAIGLAVPLD MRKYLAHVGY PRTYVDAIAE RQELEGFRIP SANGEEPES GGENDPASEL WDWWQANNLD IEATLGHTDA LIYGTAYITI SMPDPEVDFD VDPEVPLIRV EPPTALYAEV D PRTRKVLY ...String:
MAETESIDPE KLRDQLLDAF ENKQNELKSS KAYYDAERRP DAIGLAVPLD MRKYLAHVGY PRTYVDAIAE RQELEGFRIP SANGEEPES GGENDPASEL WDWWQANNLD IEATLGHTDA LIYGTAYITI SMPDPEVDFD VDPEVPLIRV EPPTALYAEV D PRTRKVLY AIRAIYGADG NEIVSATLYL PDTTMTWLRA EGEWEAPTST PHGLEMVPVI PISNRTRLSD LYGTSEISPE LR SVTDAAA QILMNMQGTA NLMAIPQRLI FGAKPEELGI NAETGQRMFD AYMARILAFE GGEGAHAEQF SAAELRNFVD ALD ALDRKA ASYSGLPPQY LSSSSDNPAS AEAIKAAESR LVKKVERKNK IFGGAWEQAM RLAYKMVKGG DIPTEYYRME TVWR DPSTP TYAAKADAAA KLFANGAGLI PRERGWVDMG YTIVEREQMR QWLEQDQKQG LGLIGSLYGA STPEGKPGEA PVGEP PAPE PDAA

UniProtKB: Portal protein

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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 / 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: GATAN K3 (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 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: 3.5 Å / Resolution method: OTHER / Number images used: 33132
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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