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- EMDB-67168: Cryo-EM structure of bacteriophage Avs-1 spike -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-67168
TitleCryo-EM structure of bacteriophage Avs-1 spike
Map data
Sample
  • Virus: Aeromonas phage Avs-1 (virus)
KeywordsComplex / VIRAL PROTEIN
Biological speciesAeromonas phage Avs-1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsLiu JY / Liu HR
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32430020 China
National Natural Science Foundation of China (NSFC)32071209 China
CitationJournal: To Be Published
Title: Cryo-EM structure of bacteriophage Avs-1 spike
Authors: Liu JY / Liu HR
History
DepositionNov 20, 2025-
Header (metadata) releaseMay 13, 2026-
Map releaseMay 13, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67168.png

Downloads & links

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Map

FileDownload / File: emd_67168.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 240 pix.
= 299.52 Å		1.25 Å/pix.
x 240 pix.
= 299.52 Å		1.25 Å/pix.
x 240 pix.
= 299.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.248 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.427
Minimum - Maximum-0.5241306 - 1.2039725
Average (Standard dev.)0.0070060254 (±0.051051285)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 299.52002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_67168_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

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Half map: #1

Fileemd_67168_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_67168_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 : Aeromonas phage Avs-1

EntireName: Aeromonas phage Avs-1 (virus)
Components
  • Virus: Aeromonas phage Avs-1 (virus)

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Supramolecule #1: Aeromonas phage Avs-1

SupramoleculeName: Aeromonas phage Avs-1 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 3101620 / Sci species name: Aeromonas phage Avs-1 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 32.0 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

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 137034
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE
FSC plot (resolution estimation)

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