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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: 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, G.N. / Martinez, M. / Kalatzis, P.G. / Middelboe, M. / San Martin, C.
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

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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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