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- EMDB-51232: Unsymmetrized map of T5 phage tail tip complex, showing the monom... -

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Basic information

Entry
Database: EMDB / ID: EMD-51232
TitleUnsymmetrized map of T5 phage tail tip complex, showing the monomeric Tail Completion Protein p143
Map dataUnsharpened map
Sample
  • Virus: Escherichia phage T5 (virus)
KeywordsBacteriophage T5 / siphophage / tail completion protein / VIRUS
Biological speciesEscherichia phage T5 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsLinares R / Breyton C
Funding support France, 2 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-16-CE11-0027 France
Agence Nationale de la Recherche (ANR)ANR-21-CE11-0023 France
CitationJournal: To Be Published
Title: About bacteriophage tail terminator and tail completion proteins: structure of the proximal extremity of siphophage T5 tail
Authors: Linares R / Breyton C
History
DepositionAug 2, 2024-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateAug 14, 2024-
Current statusAug 14, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51232.png

Downloads & links

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Map

FileDownload / File: emd_51232.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map
Voxel sizeX=Y=Z: 1.351 Å
Density
Contour LevelBy AUTHOR: 0.0155
Minimum - Maximum-0.022549035 - 0.058732253
Average (Standard dev.)0.00051799155 (±0.0044480837)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 270.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map

Fileemd_51232_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51232_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_51232_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 : Escherichia phage T5

EntireName: Escherichia phage T5 (virus)
Components
  • Virus: Escherichia phage T5 (virus)

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Supramolecule #1: Escherichia phage T5

SupramoleculeName: Escherichia phage T5 / type: virus / ID: 1 / Parent: 0
Details: Pure T5 tails obtained by infecting E. coli F strain with the amber mutant phage T5D20am30d
NCBI-ID: 2695836 / Sci species name: Escherichia phage T5 / Sci species strain: T5D20am30d / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Escherichia coli (E. coli) / Strain: F

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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: 8
Component:
ConcentrationFormulaName
10.0 mMC4H11NO3Tris
100.0 mMNaClSodium Chloride
1.0 mMMgCl2Magnesium Chloride
1.0 mMCaCl2Calcium Chloride
GridModel: Quantifoil R2/1 / Material: COPPER/RHODIUM / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: 25mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV
Details: 3 uL of T5 tails sample were deposited on a freshly glow discharged EM grid and plunge-frozen in nitrogen-cooled liquid ethane using a ThermoFisher Mark IV Vitrobot device (100 percent ...Details: 3 uL of T5 tails sample were deposited on a freshly glow discharged EM grid and plunge-frozen in nitrogen-cooled liquid ethane using a ThermoFisher Mark IV Vitrobot device (100 percent humidity, 20 Celsius degrees, 5 s blotting time, blot force 0).
DetailsPure T5 tails obtained by infecting E. coli F strain with the amber mutant phage T5D20am30d

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9290
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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