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- EMDB-55728: Structure of bacteriophage NO16 -

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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: PLoS Pathog / Year: 2026
Title: Structure of NO16, a marine non-tailed vibriophage with an unusual symmetry-mismatched vertex arrangement.
Authors: Sara Otaegi-Ugartemendia / Gabriela N Condezo / Marta Martínez / Panos G Kalatzis / Mathias Middelboe / Carmen San Martín /
Abstract: Non-tailed phages remain underexplored in marine environments, as tailed phages have long dominated sequence and culture collections. Yet recent surveys suggest that non-tailed phages may be more ...Non-tailed phages remain underexplored in marine environments, as tailed phages have long dominated sequence and culture collections. Yet recent surveys suggest that non-tailed phages may be more abundant and have distinct impacts on microbial mortality and gene transfer. Here, we solve the structure of Vibrio anguillarum bacteriophage NO16, one of the simplest members of the Varidnaviria realm. Mass spectrometry detected at least nine different proteins in the virion, which has a pseudoT = 21 capsid similar to that of related double jelly roll (DJR) phages, but differs in the organization of minor capsid proteins, particularly those mediating membrane-capsid contacts. The DJR major capsid protein GP19 is stabilized by strong electrostatic interactions between monomers, and possibly by a cation at its base, as seen in corticovirus PM2. Localized reconstruction revealed a symmetry mismatch at the vertex, where two trimeric GP13 spikes attach to the pentameric GP14 penton base. GP13 carbohydrate-binding sites and predicted glycosylase activity point to a role in host entry. Using structural and functional predictions for its entire proteome, we propose a complete atlas of the NO16 infectious cycle.
History
DepositionNov 17, 2025-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 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
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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

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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
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Additional map: #1

Fileemd_55728_additional_1.map
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Half map: #1

Fileemd_55728_half_map_1.map
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Half map: #2

Fileemd_55728_half_map_2.map
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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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