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- EMDB-29354: Structure of Agrobacterium tumefaciens bacteriophage Milano contr... -

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Basic information

Entry
Database: EMDB / ID: EMD-29354
TitleStructure of Agrobacterium tumefaciens bacteriophage Milano contracted tail-tube
Map data
Sample
  • Virus: Agrobacterium phage Milano (virus)
    • Protein or peptide: Virion-associated protein
KeywordsMyophage / redox trigger / disulfides / VIRUS
Function / homologyVirion-associated protein
Function and homology information
Biological speciesAgrobacterium phage Milano (virus)
Methodhelical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSonani RR / Leiman PG / Wang F / Kreutzberger MAB / Sebastian A / Esteves NC / Kelly RJ / Scharf B / Egelman EH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
CitationJournal: Nat Commun / Year: 2024
Title: An extensive disulfide bond network prevents tail contraction in Agrobacterium tumefaciens phage Milano.
Authors: Sonani RR / Palmer LK / Esteves NC / Horton AA / Sebastian AL / Kelly RJ / Wang F / Kreutzberger MAB / Russell WK / Leiman PG / Scharf BE / Egelman EH
History
DepositionJan 3, 2023-
Header (metadata) releaseJan 17, 2024-
Map releaseJan 17, 2024-
UpdateFeb 7, 2024-
Current statusFeb 7, 2024Processing site: RCSB / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_29354.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.82 Å
Density
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.2934916 - 0.5480267
Average (Standard dev.)0.0025827275 (±0.019538535)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 419.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Agrobacterium phage Milano

EntireName: Agrobacterium phage Milano (virus)
Components
  • Virus: Agrobacterium phage Milano (virus)
    • Protein or peptide: Virion-associated protein

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Supramolecule #1: Agrobacterium phage Milano

SupramoleculeName: Agrobacterium phage Milano / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2557550 / Sci species name: Agrobacterium phage Milano / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Agrobacterium tumefaciens C58

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Macromolecule #1: Virion-associated protein

MacromoleculeName: Virion-associated protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage Milano (virus)
Molecular weightTheoretical: 14.673427 KDa
SequenceString:
MACNKQNGVK NILITFTDCD TQEVIGPISH EQPDDTLPTY KNCAWTNTAL TNGYVQRSAS NATMTLPVVR DLRVPLAFYQ GCAQVDVQV EKFDGTVMTL TEGAVVEPEE SDGRSVTMNI VASEIDELLP PGSLAAA

UniProtKB: Virion-associated protein

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 34.07 Å
Applied symmetry - Helical parameters - Δ&Phi: 28.21 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 160399
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8fop

Final angle assignmentType: NOT APPLICABLE

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