9QG9 | pdb_00009qg9

MDA phage capsid

  • Classification: VIRUS
  • Organism(s): Neisseria meningitidis
  • Mutation(s): No 

  • Deposited: 2025-03-13 Released: 2025-06-04 
  • Deposition Author(s): Boehning, J., Bharat, T.A.M.
  • Funding Organization(s): Medical Research Council (MRC, United Kingdom), Wellcome Trust, Leverhulme Trust, The Lister Institute of Preventive Medicine

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of the virulence-associated Neisseria meningitidis filamentous bacteriophage MDA Phi.

Bohning, J.Graham, M.Coureuil, M.Tarafder, A.K.Meyer, J.Nassif, X.Bille, E.Bharat, T.A.M.

(2025) Proc Natl Acad Sci U S A 122: e2420157122-e2420157122

  • DOI: https://doi.org/10.1073/pnas.2420157122
  • Primary Citation of Related Structures:  
    9QG9

  • PubMed Abstract: 

    Neisseria meningitidis is a human commensal bacterium that can opportunistically invade the bloodstream and cross the blood-brain barrier, where it can cause septicemia and meningitis. These diseases, if left untreated, can be lethal within hours. Hyperinvasive N. meningitidis strains often express a genomically encoded filamentous bacteriophage called MDAΦ, which promotes colonization of mucosal host surfaces to facilitate bacterial invasion. How this phage is organized and how it promotes biofilm formation and infection at the molecular level is unclear. Here, we present an electron cryomicroscopy structure of the MDA phage, showing that MDAΦ is a class I filamentous inovirus, with the major capsid protein (MCP) arranged within the phage as a highly curved and densely packed α-helix. Comparison with other filamentous bacteriophages offers clues about inoviral genome encapsidation mechanisms, providing a framework for understanding the evolutionary diversity of inoviruses. A disordered, N-terminal segment in the MCP presents hydrophobic patches on the surface of assembled phage particles, which, together with electron cryotomography data of phage bundles, furnishes a structural rationale for phage-phage interactions that were seen previously in an epithelium adhesion infection model of N. meningitidis . Taken together, our results shed light on the structure, organization, and higher-order assembly of a biomedically relevant phage encoded in the genome of a human pathogen. Molecular insights gleaned from this study increase our understanding of phage evolution, phage-mediated bacterial adhesion, and pathogenicity.


  • Organizational Affiliation
    • Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Integral membrane proteinA [auth 9]51Neisseria meningitidisMutation(s): 0 
UniProt
Find proteins for A0A0U1RJP7 (Neisseria meningitidis serogroup A / serotype 4A (strain DSM 15465 / Z2491))
Explore A0A0U1RJP7 
Go to UniProtKB:  A0A0U1RJP7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0U1RJP7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION4
MODEL REFINEMENTServalcat

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC_UP_1201/31
Wellcome TrustUnited Kingdom225317/Z/22/Z
Leverhulme TrustUnited Kingdom--
The Lister Institute of Preventive MedicineUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-04
    Type: Initial release
  • Version 1.1: 2025-07-02
    Changes: Data collection, Database references