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- PDB-9t9r: Structure of bacteriophage NO16 -

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Basic information

Entry
Database: PDB / ID: 9t9r
TitleStructure of bacteriophage NO16
Components
  • Penton base (GP14)
  • Spike (GP13)
KeywordsVIRUS / non-tailed vibriophage / marine virus
Function / homologyUncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesVibrio phage fNo16 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 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
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, 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: Penton base (GP14)
H: Spike (GP13)
G: Spike (GP13)
F: Spike (GP13)
E: Penton base (GP14)
B: Penton base (GP14)
C: Penton base (GP14)
D: Penton base (GP14)


Theoretical massNumber of molelcules
Total (without water)175,1348
Polymers175,1348
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Penton base (GP14)


Mass: 19919.262 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Vibrio phage fNo16 (virus) / References: UniProt: A0A3G1SVM6
#2: Protein Spike (GP13)


Mass: 25179.096 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Vibrio phage fNo16 (virus) / References: UniProt: A0A3G1SVP4
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: all / Source: NATURAL
Source (natural)Organism: Vibrio phage fNo16 (virus)
Details of virusEmpty: NO / Enveloped: YES / 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: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 162312 / Symmetry type: POINT

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