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- EMDB-55728: Structure of bacteriophage NO16 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-55728
TitleStructure of bacteriophage NO16
Map data
Sample
  • Virus: Vibrio phage fNo16 (virus)
    • Protein or peptide: Penton base (GP14)
    • Protein or peptide: Spike (GP13)
Keywordsnon-tailed vibriophage / marine virus / VIRUS
Function / homologyUncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesVibrio phage fNo16 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsOtaegi-Ugartemendia S / Condezo GN / Martinez M / Kalatzis PG / Middelboe M / San Martin C
Funding support Spain, European Union, Denmark, 10 items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)AEI/10.13039/501100011033 Spain
European Regional Development FundPID2019-104098GB-I00European Union
European Regional Development FundPID2022-136456NB-I00European Union
Agencia Estatal de Investigacion (AEI)SEV-2017-0712 Spain
Agencia Estatal de Investigacion (AEI)CEX2023-001386-S Spain
Other governmentJAE-SOMdM20-20
Spanish Ministry of Science, Innovation, and UniversitiesFPU2020-05148 Spain
European Union (EU)101084204European Union
Other government2105-00014B
Danish National Research FoundationDNRF145 Denmark
CitationJournal: To Be Published / Year: 2026
Title: Structure of NO16, a marine non-tailed vibriophage with an unusual symmetry-mismatched vertex arrangement
Authors: Otaegi-Ugartemendia S / Condezo GN / Martinez M / Kalatzis PG / Middelboe M / San Martin C
History
DepositionNov 17, 2025-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55728.png

Downloads & links

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Map

FileDownload / File: emd_55728.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 320 pix.
= 428.8 Å		1.34 Å/pix.
x 320 pix.
= 428.8 Å		1.34 Å/pix.
x 320 pix.
= 428.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.09316967 - 0.14766496
Average (Standard dev.)0.00003110122 (±0.0016386547)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 428.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55728_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_55728_additional_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55728_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_55728_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Vibrio phage fNo16

EntireName: Vibrio phage fNo16 (virus)
Components
  • Virus: Vibrio phage fNo16 (virus)
    • Protein or peptide: Penton base (GP14)
    • Protein or peptide: Spike (GP13)

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Supramolecule #1: Vibrio phage fNo16

SupramoleculeName: Vibrio phage fNo16 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2315335 / Sci species name: Vibrio phage fNo16 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Vibrio anguillarum (bacteria) / Strain: A023
Virus shellShell ID: 1 / Name: Icosahedral capsid / T number (triangulation number): 21

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Macromolecule #1: Penton base (GP14)

MacromoleculeName: Penton base (GP14) / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Vibrio phage fNo16 (virus)
Molecular weightTheoretical: 19.919262 KDa
SequenceString:
MSVTTVTAKP VPAVIATSGR NFQLLSGGEV TVKFYGVNGD WEEEVELSVG DSLEFEQRFA RFTVQTQYET RVSFYSGFAK MRRSKQDLV VTGTTSIKTS QKQVTKVESM LIEPNRNRRN VVVFPLNDTI YVGGLGTSQN DKLPVPVGGS ITLDTQAAIY V TQDQSSAN DFADVRILEE FN

UniProtKB: Uncharacterized protein

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Macromolecule #2: Spike (GP13)

MacromoleculeName: Spike (GP13) / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Vibrio phage fNo16 (virus)
Molecular weightTheoretical: 25.179096 KDa
SequenceString: MAVLSGFPQN VTYQSVTVAQ GGGSENLLIN PRGKINQANE SAGVLAAGQY FCDGWKAGGS GAEVYIDADG FRLVSGSILQ LVPNNLESG RSIRGNMDAI MGNPVISING GSDNELSDSA QYIQFEISGN NSKFTRIVLA ESVSAPIYQQ LSDELKHCKR F LFVSESNQ ...String:
MAVLSGFPQN VTYQSVTVAQ GGGSENLLIN PRGKINQANE SAGVLAAGQY FCDGWKAGGS GAEVYIDADG FRLVSGSILQ LVPNNLESG RSIRGNMDAI MGNPVISING GSDNELSDSA QYIQFEISGN NSKFTRIVLA ESVSAPIYQQ LSDELKHCKR F LFVSESNQ ELYSALSAYS FVSYQFDEMH IPPAVTVGQL YQGSQIFQVS KNKVMFLKSG SSSTAGFTGG IKLDARP

UniProtKB: Uncharacterized protein

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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: 7.2
GridMaterial: COPPER/RHODIUM
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 39.97 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 162312
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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