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- EMDB-55739: Structure of bacteriophage NO16 -

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Basic information

Entry
Database: EMDB / ID: EMD-55739
TitleStructure of bacteriophage NO16
Map data
Sample
  • Virus: Vibrio phage fNo16 (virus)
    • Protein or peptide: Double jelly roll capsid protein
    • Protein or peptide: Penton base (GP14)
    • Protein or peptide: LPXTG cell wall anchor domain-containing protein
    • Protein or peptide: Unknown1
  • Ligand: UNKNOWN LIGAND
Keywordsnon-tailed vibriophage / marine virus / VIRUS
Function / homologyViral coat protein P2, N-terminal / : / : / Viral coat protein P2 N-terminal domain / Viral coat protein P2 C-terminal domain / Double jelly roll capsid protein / Uncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesVibrio phage fNo16 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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
Ministerio de Ciencia e Innovacion (MCIN)FPU2020-05148 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_55739.png

Downloads & links

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Map

FileDownload / File: emd_55739.map.gz / Format: CCP4 / Size: 2.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 900 pix.
= 1206. Å		1.34 Å/pix.
x 900 pix.
= 1206. Å		1.34 Å/pix.
x 900 pix.
= 1206. 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: 0.01
Minimum - Maximum-0.046775445 - 0.07822975
Average (Standard dev.)-0.0022804295 (±0.0042320346)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-450-450-450
Dimensions900900900
Spacing900900900
CellA=B=C: 1206.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_55739_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_55739_half_map_2.map
Projections & Slices
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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: Double jelly roll capsid protein
    • Protein or peptide: Penton base (GP14)
    • Protein or peptide: LPXTG cell wall anchor domain-containing protein
    • Protein or peptide: Unknown1
  • Ligand: UNKNOWN LIGAND

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Supramolecule #1: Vibrio phage fNo16

SupramoleculeName: Vibrio phage fNo16 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / NCBI-ID: 2315335 / Sci species name: Vibrio phage fNo16 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / 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: Double jelly roll capsid protein

MacromoleculeName: Double jelly roll capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Vibrio phage fNo16 (virus)
Molecular weightTheoretical: 29.037104 KDa
SequenceString: MARITRKMPS FSNVAAGSTA TLEFPLGLSY HFLHLYFTGV TLAQMKNIRI EVDGKPIKKW ADGVRLNAEN KHYGRGAATA DCLPIWFVR KELTELAQQR LFALGTSNVQ TMSLLIDIDE AAASPVLKAT SKRGPQDVMG YITRIHEFKH SSAVSGEIEI D NIPLRTGA ...String:
MARITRKMPS FSNVAAGSTA TLEFPLGLSY HFLHLYFTGV TLAQMKNIRI EVDGKPIKKW ADGVRLNAEN KHYGRGAATA DCLPIWFVR KELTELAQQR LFALGTSNVQ TMSLLIDIDE AAASPVLKAT SKRGPQDVMG YITRIHEFKH SSAVSGEIEI D NIPLRTGA AIAAIHIYSA DVTDCALEID GAIVWEMSKA GSAKEQVDHG RDPQTASKLT LDFLLEGDFF QGVALDGIQD FR LKPTLSA AGNMDIVVEY TETYNPKA

UniProtKB: Double jelly roll capsid protein

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Macromolecule #2: Penton base (GP14)

MacromoleculeName: Penton base (GP14) / type: protein_or_peptide / ID: 2 / Number of copies: 1 / 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 #3: LPXTG cell wall anchor domain-containing protein

MacromoleculeName: LPXTG cell wall anchor domain-containing protein / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Vibrio phage fNo16 (virus)
Molecular weightTheoretical: 8.745928 KDa
SequenceString:
MFDDFLGDFQ LKDAVGAWLA NEQIKRVDDA TGQSQSEVYN TPNKTQQVNG TVTTNATGGL SMPVLMGAGA VGLVLLVLLI RK

UniProtKB: Uncharacterized protein

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Macromolecule #4: Unknown1

MacromoleculeName: Unknown1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio phage fNo16 (virus)
Molecular weightTheoretical: 1.039273 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

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Macromolecule #5: UNKNOWN LIGAND

MacromoleculeName: UNKNOWN LIGAND / type: ligand / ID: 5 / Number of copies: 4 / Formula: UNX
Chemical component information


ChemComp, No image

ChemComp-UNL:
Unknown ligand

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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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 15429
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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