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- EMDB-49081: Tail tube structure of Acinetobacter baumannii phage Mystique -

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Basic information

Entry
Database: EMDB / ID: EMD-49081
TitleTail tube structure of Acinetobacter baumannii phage Mystique
Map data
SampleMystique != Acinetobacter phage Mystique

Mystique

  • Virus: Acinetobacter phage Mystique (virus)
    • Protein or peptide: Tail tube
KeywordsTail tube / tail / helical / tail tube protein / phage / bacteriophage / VIRAL PROTEIN
Biological speciesAcinetobacter phage Mystique (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsKopylov M / Bobe D / Alseth OE
Funding support United States, 1 items
OrganizationGrant numberCountry
Simons FoundationSF349247 United States
CitationJournal: Biorxiv / Year: 2024
Title: Tail tube structure of Acinetobacter baumannii phage Mystique
Authors: Alseth OE / Roush C / Irby I / Kopylov M / Bobe D / Nguyen K / Xu H / Bryksin A / Rather NP
History
DepositionFeb 5, 2025-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49081.png

Downloads & links

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Map

FileDownload / File: emd_49081.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 360 pix.
= 389.88 Å		1.08 Å/pix.
x 360 pix.
= 389.88 Å		1.08 Å/pix.
x 360 pix.
= 389.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.083 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-2.3998494 - 3.7741344
Average (Standard dev.)0.008138447 (±0.15935043)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 389.87997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49081_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49081_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49081_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mystique

EntireName: Mystique (virus)
Components
  • Virus: Acinetobacter phage Mystique (virus)
    • Protein or peptide: Tail tube

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Supramolecule #1: Acinetobacter phage Mystique

SupramoleculeName: Acinetobacter phage Mystique / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 3373405 / Sci species name: Acinetobacter phage Mystique / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Acinetobacter baumannii (bacteria) / Strain: AB5075
Virus shellShell ID: 1 / T number (triangulation number): 9

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Macromolecule #1: Tail tube

MacromoleculeName: Tail tube / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter phage Mystique (virus)
Molecular weightTheoretical: 27.983414 KDa
SequenceString: MQQNFGTALG DGFVLNEATL MIGALGSALD LTEEEHSVGL FKNLAIANDK TFQDLNQGVT QDTVHSQKTG DNWTISGNGY EYNPRTIMY ALGQAGFTAD PTAARTRAVV SAPAAVGVSE ISVQSATGLA VGDWVILYNK LGDNNGLAYK IDAIATNTIT L DRDLVAPV ...String:
MQQNFGTALG DGFVLNEATL MIGALGSALD LTEEEHSVGL FKNLAIANDK TFQDLNQGVT QDTVHSQKTG DNWTISGNGY EYNPRTIMY ALGQAGFTAD PTAARTRAVV SAPAAVGVSE ISVQSATGLA VGDWVILYNK LGDNNGLAYK IDAIATNTIT L DRDLVAPV AVGDELVKST LINTNNPNSC SGAEYFSAKI VSADVNCNPI VVIVPKVQIT SGLNLAFGAT DYANIAYQMK AM ALTRKDA GYDLYVQHGK SKVFLLT

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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

BufferpH: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k 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: 2.0 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 191000
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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