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- PDB-9qg9: MDA phage capsid -

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Basic information

Entry
Database: PDB / ID: 9qg9
TitleMDA phage capsid
ComponentsIntegral membrane protein
KeywordsVIRUS / bacteriophage / capsid / neisseria / MCP / major capsid protein / filamentous bacteriophage / inovirus
Function / homologymembrane / Integral membrane protein
Function and homology information
Biological speciesNeisseria meningitidis (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsBoehning, J. / Bharat, T.A.M.
Funding support United Kingdom, 4items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
9: Integral membrane protein


Theoretical massNumber of molelcules
Total (without water)5,2351
Polymers5,2351
Non-polymers00
Water00
1
9: Integral membrane protein
x 55


Theoretical massNumber of molelcules
Total (without water)287,94155
Polymers287,94155
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation1_555x,y,z1
point symmetry operation53
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.739902, 0.672714), (-0.672714, 0.739902), (1)-101.9988, 230.5911, -14.1313
3generate(0.868432, -0.495809), (0.495809, 0.868432), (1)155.0876, -90.0403, -14.1313
4generate(0.976092, 0.217356), (-0.217356, 0.976092), (1)-47.8205, 59.6404, -28.2626
5generate(0.575994, 0.817454), (-0.817454, 0.575994), (1)-97.2604, 306.8887, -42.3939

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Components

#1: Protein Integral membrane protein


Mass: 5235.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neisseria meningitidis (bacteria) / Strain: Z5463 / References: UniProt: A0A0U1RJP7
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: MDA / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: MDA (bacteria)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Neisseria meningitidis / Strain: Z5463
Buffer solutionpH: 7.4 / Details: PBS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil
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: 1000 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 41 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4RELION4CTF correction
7PHENIXmodel fitting
10RELION4final Euler assignment
12RELION43D reconstruction
13Servalcatmodel refinement
CTF correctionDetails: RELION CTF Correction / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 42.2769 ° / Axial rise/subunit: 14.1313 Å / Axial symmetry: C5
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27134 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL / Details: PHENIX and Servalcat was used
RefinementResolution: 3.7→138.43 Å / Cor.coef. Fo:Fc: 0.923 / SU B: 45.1 / SU ML: 0.618 / ESU R: 0.207
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.44319 --
obs0.44319 24310 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 169.057 Å2
Refinement stepCycle: 1 / Total: 363
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.012367
ELECTRON MICROSCOPYr_bond_other_d0.0010.015382
ELECTRON MICROSCOPYr_angle_refined_deg1.5811.705494
ELECTRON MICROSCOPYr_angle_other_deg0.7051.707871
ELECTRON MICROSCOPYr_dihedral_angle_1_deg9.427550
ELECTRON MICROSCOPYr_dihedral_angle_2_deg
ELECTRON MICROSCOPYr_dihedral_angle_3_deg14.9771064
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0910.262
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.02413
ELECTRON MICROSCOPYr_gen_planes_other0.0040.0277
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it13.4716.617203
ELECTRON MICROSCOPYr_mcbond_other13.42816.621203
ELECTRON MICROSCOPYr_mcangle_it23.40729.665252
ELECTRON MICROSCOPYr_mcangle_other23.36129.729253
ELECTRON MICROSCOPYr_scbond_it11.57417.775164
ELECTRON MICROSCOPYr_scbond_other11.53917.847165
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other21.94332.584243
ELECTRON MICROSCOPYr_long_range_B_refined33.346174.92462
ELECTRON MICROSCOPYr_long_range_B_other33.314175.08463
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.7→3.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.628 1733 -
obs--100 %

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