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- EMDB-46685: Mycobacteriophage Bxb1 Capsid - Composite map and model -

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Basic information

Entry
Database: EMDB / ID: EMD-46685
TitleMycobacteriophage Bxb1 Capsid - Composite map and model
Map dataMycobacteriophage Bxb1 Capsid - Composite map and model
Sample
  • Virus: Mycobacterium phage Bxb1 (virus)
    • Protein or peptide: Major capsid protein
KeywordsBacteriophage / capsid / VIRUS / VIRAL PROTEIN
Function / homologyPhage capsid / Phage capsid family / Major capsid protein
Function and homology information
Biological speciesMycobacterium phage Bxb1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 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: To Be Published
Title: Structure and infection dynamics of mycobacteriophage Bxb1
Authors: Freeman KG / Mondal S / Macale LS / Podgorski J / White SJ / Silva B / Ortiz V / Huet A / Narsico JT / Ho MC / Jacobs-Sera D / Lowary TL / Conway JF / Park D / Hatfull GF
History
DepositionAug 21, 2024-
Header (metadata) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateSep 25, 2024-
Current statusSep 25, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46685.png

Downloads & links

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Map

FileDownload / File: emd_46685.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMycobacteriophage Bxb1 Capsid - Composite map and model
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (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: 4.0
Minimum - Maximum-11.088003 - 37.326700000000002
Average (Standard dev.)0.000000000000164 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 1056.0 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

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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: 11 / 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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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 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) / Detector mode: COUNTING / 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

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: OTHER / Number images used: 23927
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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