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- PDB-9t9v: Structure of bacteriophage NO16 -

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Basic information

Entry
Database: PDB / ID: 9t9v
TitleStructure of bacteriophage NO16
Components
  • Double jelly roll capsid protein
  • LPXTG cell wall anchor domain-containing protein
  • Penton base (GP14)
  • Unknown1
KeywordsVIRUS / non-tailed vibriophage / marine 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsOtaegi-Ugartemendia, S. / Condezo, G.N. / Martinez, M. / Kalatzis, P.G. / Middelboe, M. / San Martin, C.
Funding support Spain, European Union, Denmark, 10items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Sep 23, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Double jelly roll capsid protein
B: Double jelly roll capsid protein
C: Double jelly roll capsid protein
D: Double jelly roll capsid protein
E: Double jelly roll capsid protein
F: Double jelly roll capsid protein
G: Double jelly roll capsid protein
H: Double jelly roll capsid protein
I: Double jelly roll capsid protein
J: Double jelly roll capsid protein
K: Penton base (GP14)
L: LPXTG cell wall anchor domain-containing protein
M: LPXTG cell wall anchor domain-containing protein
N: LPXTG cell wall anchor domain-containing protein
O: Unknown1


Theoretical massNumber of molelcules
Total (without water)337,56719
Polymers337,56715
Non-polymers04
Water00
1
A: Double jelly roll capsid protein
B: Double jelly roll capsid protein
C: Double jelly roll capsid protein
D: Double jelly roll capsid protein
E: Double jelly roll capsid protein
F: Double jelly roll capsid protein
G: Double jelly roll capsid protein
H: Double jelly roll capsid protein
I: Double jelly roll capsid protein
J: Double jelly roll capsid protein
K: Penton base (GP14)
L: LPXTG cell wall anchor domain-containing protein
M: LPXTG cell wall anchor domain-containing protein
N: LPXTG cell wall anchor domain-containing protein
O: Unknown1
x 60


Theoretical massNumber of molelcules
Total (without water)20,254,0421140
Polymers20,254,042900
Non-polymers0240
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein
Double jelly roll capsid protein


Mass: 29037.104 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Vibrio phage fNo16 (virus) / References: UniProt: A0A3G1SVL0
#2: Protein Penton base (GP14)


Mass: 19919.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio phage fNo16 (virus) / References: UniProt: A0A3G1SVM6
#3: Protein LPXTG cell wall anchor domain-containing protein


Mass: 8745.928 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Vibrio phage fNo16 (virus) / References: UniProt: A0A3G1SVN4
#4: Protein/peptide Unknown1


Mass: 1039.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio phage fNo16 (virus)
#5: Chemical
ChemComp-UNX / UNKNOWN LIGAND


Num. of mol.: 4 / Source method: obtained synthetically
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Vibrio phage fNo16 / Type: VIRUS / Entity ID: #1-#4 / Source: NATURAL
Source (natural)Organism: Vibrio phage fNo16 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Vibrio anguillarum / Strain: A023
Virus shellName: Icosahedral capsid / Triangulation number (T number): 21
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 39.97 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1Xmippparticle selection
2EPU3.5.1image acquisition
4CTFFINDCTF correction
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15429 / Symmetry type: POINT

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