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- EMDB-58047: Head-proximal tail tube segment of Lactococcus phage Nocturne116 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-58047
TitleHead-proximal tail tube segment of Lactococcus phage Nocturne116
Map data
Sample
  • Virus: Lactococcus phage Nocturne116 (virus)
KeywordsBacteriophage / tail / neck / VIRUS
Biological speciesLactococcus phage Nocturne116 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.31 Å
AuthorsRumnieks J / Tars K
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Union (EU)5.2.1.1.i.0/2/24/I/CFLA/001European Union
CitationJournal: To Be Published
Title: Three-dimensional structure of Lactococcus bacteriophage Nocturne116
Authors: Rumnieks J / Tars K
History
DepositionMay 13, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58047.png

Downloads & links

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Map

FileDownload / File: emd_58047.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.78 Å/pix.
x 420 pix.
= 328.86 Å		0.78 Å/pix.
x 420 pix.
= 328.86 Å		0.78 Å/pix.
x 420 pix.
= 328.86 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.783 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0055
Minimum - Maximum-0.0043404903 - 0.015355095
Average (Standard dev.)0.00020332531 (±0.0010237498)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 328.86 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_58047_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_58047_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_58047_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 : Lactococcus phage Nocturne116

EntireName: Lactococcus phage Nocturne116 (virus)
Components
  • Virus: Lactococcus phage Nocturne116 (virus)

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Supramolecule #1: Lactococcus phage Nocturne116

SupramoleculeName: Lactococcus phage Nocturne116 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 2831179 / Sci species name: Lactococcus phage Nocturne116 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Lactococcus lactis (lactic acid bacteria) / Strain: LNT

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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

Concentration3 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMTris-HCl
100.0 mMsodium chlorideNaCl
10.0 mMmagnesium sulfateMgSO4
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: GRAPHENE / Support film - #1 - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-40 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 165000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Low-pass filtered previous reconstruction
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.31 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0.0) / Number images used: 4539
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0.0)
FSC plot (resolution estimation)

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