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- EMDB-67163: Cryo-EM structure of bacteriophage Avs-1 capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-67163
TitleCryo-EM structure of bacteriophage Avs-1 capsid
Map data
Sample
  • Virus: Aeromonas phage Avs-1 (virus)
    • Protein or peptide: Major capsid protein
KeywordsComplex / VIRAL PROTEIN
Biological speciesAeromonas phage avSL1 (virus) / Aeromonas phage Avs-1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 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 capsid
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_67163.png

Downloads & links

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Map

FileDownload / File: emd_67163.map.gz / Format: CCP4 / Size: 1.3 GB / 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 700 pix.
= 873.6 Å		1.25 Å/pix.
x 700 pix.
= 873.6 Å		1.25 Å/pix.
x 700 pix.
= 873.6 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: 0.635
Minimum - Maximum-0.5237271 - 1.7617184
Average (Standard dev.)0.016220806 (±0.13466144)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions700700700
Spacing700700700
CellA=B=C: 873.60004 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_67163_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_67163_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_67163_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)
    • Protein or peptide: Major capsid protein

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Supramolecule #1: Aeromonas phage Avs-1

SupramoleculeName: Aeromonas phage Avs-1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / 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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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Aeromonas phage avSL1 (virus)
SequenceString: MTLEELKALI EKATANFEAQ KKENAELTVQ IKAQEEKFTQ LKGEFDKLKE GGDQDEAKKM AKDLEELAN EISDLRSKYK APAAVVTEDQ KKAMHDAILK PVIGEWLKGK RNNTAPEFFK F IEQQGTER FKTLNLTNAD EGGRAVAEVL SRDVIEYARE YSPVLGQVGR ...String:
MTLEELKALI EKATANFEAQ KKENAELTVQ IKAQEEKFTQ LKGEFDKLKE GGDQDEAKKM AKDLEELAN EISDLRSKYK APAAVVTEDQ KKAMHDAILK PVIGEWLKGK RNNTAPEFFK F IEQQGTER FKTLNLTNAD EGGRAVAEVL SRDVIEYARE YSPVLGQVGR KPSMTRNFRE LV LVTYPSV AEGIENVAGT DFAETTTQEY KEVKSKEFKV SAKPRITDEA MYGADIDLYG DLV RLLGRE ISIYLAAQVL YGNGTGKNAR GILSSKRVDI TDGTGKSWLP TLAADPANAR PADY YPAVS TGVAGDLGAD DTARVNFIVD LVNKLPTQWL PGAKFHMNRK VKGMLEKIRD ENNKP VFMN SYREGDGFML MGFPVVIDDT LPNLTANSTP IIFGNLGAAY AINDGDIDKM LIDPYT VDD CTVVKYSKEM FEMVQNSDAI LIVAATTNDG TV

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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: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 44943
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE
FSC plot (resolution estimation)

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