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- EMDB-53129: MDA phage capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-53129
TitleMDA phage capsid
Map data
Sample
  • Virus: MDA (bacteria)
    • Protein or peptide: Integral membrane protein
Keywordsbacteriophage / capsid / neisseria / MCP / major capsid protein / filamentous bacteriophage / inovirus / VIRUS
Function / homologymembrane / Integral membrane protein
Function and homology information
Biological speciesNeisseria meningitidis (bacteria) / MDA (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsBoehning J / Bharat TAM
Funding support United Kingdom, 4 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_1201/31 United Kingdom
Wellcome Trust225317/Z/22/Z United Kingdom
Leverhulme Trust United Kingdom
The Lister Institute of Preventive Medicine United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Structure of the virulence-associated filamentous bacteriophage MDAΦ.
Authors: Jan Böhning / Miles Graham / Mathieu Coureuil / Abul K Tarafder / Julie Meyer / Xavier Nassif / Emmanuelle Bille / Tanmay A M Bharat /
Abstract: 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, ... 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 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 . 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.
History
DepositionMar 13, 2025-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53129.png

Downloads & links

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Map

FileDownload / File: emd_53129.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 400 pix.
= 494.4 Å		1.24 Å/pix.
x 400 pix.
= 494.4 Å		1.24 Å/pix.
x 400 pix.
= 494.4 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.236 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0125
Minimum - Maximum-0.023942523 - 0.04229084
Average (Standard dev.)0.0000791044 (±0.0014791491)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 494.39996 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53129_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_53129_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_53129_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : MDA

EntireName: MDA (bacteria)
Components
  • Virus: MDA (bacteria)
    • Protein or peptide: Integral membrane protein

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Supramolecule #1: MDA

SupramoleculeName: MDA / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 487 / Sci species name: MDA / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Neisseria meningitidis (bacteria) / Strain: Z5463

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Macromolecule #1: Integral membrane protein

MacromoleculeName: Integral membrane protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Neisseria meningitidis (bacteria) / Strain: Z5463
Molecular weightTheoretical: 5.235297 KDa
SequenceString:
DGFDAAAIGT QVANVIMGFV AMVSAVGMAA ITVILAIQGF KMAWSMIKSV K

UniProtKB: Integral membrane protein

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.4 / Details: PBS
GridModel: Quantifoil / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 41.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 14.1313 Å
Applied symmetry - Helical parameters - Δ&Phi: 42.2769 °
Applied symmetry - Helical parameters - Axial symmetry: C5 (5 fold cyclic)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 27134
CTF correctionSoftware - Name: RELION (ver. 4) / Details: RELION CTF Correction / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Cylindrical reference
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 4)
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsPHENIX and Servalcat was used
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9qg9:
MDA phage capsid

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