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 9T9R | pdb_00009t9r

Structure of bacteriophage NO16


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9T9R

This is version 1.1 of the entry. See complete history. 

Literature

Structure of NO16, a marine non-tailed vibriophage with an unusual symmetry-mismatched vertex arrangement.

Otaegi-Ugartemendia, S., Condezo, G.N., Martinez, M., Kalatzis, P.G., Middelboe, M., San Martin, C.

(2026) PLoS Pathog 22: e1014525-e1014525

  • DOI: https://doi.org/10.1371/journal.ppat.1014525
  • Primary Citation Related Structures: 
    9T9R, 9T9V

  • PubMed 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 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.


  • Organizational Affiliation: 
    • Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.

Macromolecule Content 

  • Total Structure Weight: 175.13 kDa 
  • Atom Count: 6,877 
  • Modeled Residue Count: 893 
  • Deposited Residue Count: 1,605 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Penton base (GP14)A,
E,
F [auth B],
G [auth C],
H [auth D]
180Vibrio phage fNo16Mutation(s): 0 
UniProt
Find proteins for A0A3G1SVM6 (Vibrio phage fNo16)
Explore A0A3G1SVM6 
Go to UniProtKB:  A0A3G1SVM6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3G1SVM6
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike (GP13)B [auth H],
C [auth G],
D [auth F]
235Vibrio phage fNo16Mutation(s): 0 
UniProt
Find proteins for A0A3G1SVP4 (Vibrio phage fNo16)
Explore A0A3G1SVP4 
Go to UniProtKB:  A0A3G1SVP4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3G1SVP4
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agencia Estatal de Investigacion (AEI)SpainAEI/10.13039/501100011033
European Regional Development FundEuropean UnionPID2019-104098GB-I00
European Regional Development FundEuropean UnionPID2022-136456NB-I00
Agencia Estatal de Investigacion (AEI)SpainSEV-2017-0712
Agencia Estatal de Investigacion (AEI)SpainCEX2023-001386-S
Other governmentJAE-SOMdM20-20
Spanish Ministry of Science, Innovation, and UniversitiesSpainFPU2020-05148
European Union (EU)European Union101084204
Other government2105-00014B
Danish National Research FoundationDenmarkDNRF145

Revision History  (Full details and data files)

  • Version 1.0: 2026-08-19
    Type: Initial release
  • Version 1.1: 2026-09-23
    Changes: Data collection, Database references