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- EMDB-62019: The structure of Microviridae PJNS001 -

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Basic information

Entry
Database: EMDB / ID: EMD-62019
TitleThe structure of Microviridae PJNS001
Map data
Sample
  • Virus: Microviridae (isometric ssDNA phages)
    • Protein or peptide: Capsid protein F
    • Protein or peptide: Major spike protein G
    • Protein or peptide: DNA-binding protein J
Keywordsstructual proteins / VIRUS
Function / homology
Function and homology information


symbiont-mediated perturbation of host process / T=1 icosahedral viral capsid / viral capsid / host cell cytoplasm / symbiont entry into host cell / virion attachment to host cell / structural molecule activity / DNA binding
Similarity search - Function
Microvirus J protein-like / Microvirus J protein / Major spike protein G / Major spike protein (G protein) / Microviridae F protein / Microviridae F protein superfamily / Capsid protein (F protein) / Capsid/spike protein, ssDNA virus / Viral coat protein subunit
Similarity search - Domain/homology
Major spike protein G / DNA-binding protein J / Capsid protein F
Similarity search - Component
Biological speciesMicroviridae (isometric ssDNA phages)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsHu WL / Chen YB / Wei YM / Gao Y
Funding support1 items
OrganizationGrant numberCountry
Other government23QA1406400
CitationJournal: Commun Biol / Year: 2025
Title: Structural basis for Salmonella infection by two Microviridae phages.
Authors: Wanlong Hu / Zhengjie Liu / Yuming Wei / Qucheng Bian / Weiqi Lan / Chongzheng Fan / Jiaoyang Song / Qianqian Sun / Xiaojie Zhang / Yuqing Liu / Yan Gao / Yibao Chen /
Abstract: The global resurgence of multidrug-resistant Salmonella species, responsible for millions of annual infections, underscores the urgent need for alternative antimicrobial strategies, such as phage ...The global resurgence of multidrug-resistant Salmonella species, responsible for millions of annual infections, underscores the urgent need for alternative antimicrobial strategies, such as phage therapy. Microviridae phages offer a promising model for studying phage-host interactions with their unique structural and infection mechanisms. Here, we identify two Microviridae phages, PJNS001 and PJNS002, with different host receptor dependencies, and determine their cryo-EM structures at 2.68 Å and 2.59 Å resolution, respectively. These icosahedral capsids with T = 1 symmetry exhibit a unique vertex reinforcement mechanism, stabilizing the viral assembly. The specific pentameric adaptations, coupled with DNA binding protein engagements and thermodynamic constraints, collectively preclude the formation of hybrid virions. Structural analysis and in situ visualization reveal spike protein features and host-attachment intermediates, informing host specificity. Together, these findings advance our understanding of Microviridae infection mechanisms and provide a structural framework for rational phage design against antibiotic-resistant pathogens.
History
DepositionOct 19, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62019.png

Downloads & links

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Map

FileDownload / File: emd_62019.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-1.7925357 - 4.0883703
Average (Standard dev.)0.087751664 (±0.28139192)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 423.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62019_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62019_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Microviridae

EntireName: Microviridae (isometric ssDNA phages)
Components
  • Virus: Microviridae (isometric ssDNA phages)
    • Protein or peptide: Capsid protein F
    • Protein or peptide: Major spike protein G
    • Protein or peptide: DNA-binding protein J

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Supramolecule #1: Microviridae

SupramoleculeName: Microviridae / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: T=1 icosahedral virus / NCBI-ID: 10841 / Sci species name: Microviridae / Sci species strain: PJNS001 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Salmonella (bacteria)
Molecular weightTheoretical: 4.31 MDa
Virus shellShell ID: 1 / Diameter: 290.0 Å / T number (triangulation number): 1

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Macromolecule #1: Capsid protein F

MacromoleculeName: Capsid protein F / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Microviridae (isometric ssDNA phages) / Strain: PJNS001
Molecular weightTheoretical: 48.50048 KDa
SequenceString: MSNVQTGAER MPHDLSHLGF LAGQIGRLIT ISTTPVIAGD SFEMDAVGAL RLSPLRRGLA IDSTVDIFTF YVPHRHVYGE QWIKFMKDG VNAAPLPTVN TTGYIDHAAF LGTINPDTNK IPKHLFQGYL NIYNNYFKAP WMPDRTEANP NQLNEDDARY G FRCCHLKN ...String:
MSNVQTGAER MPHDLSHLGF LAGQIGRLIT ISTTPVIAGD SFEMDAVGAL RLSPLRRGLA IDSTVDIFTF YVPHRHVYGE QWIKFMKDG VNAAPLPTVN TTGYIDHAAF LGTINPDTNK IPKHLFQGYL NIYNNYFKAP WMPDRTEANP NQLNEDDARY G FRCCHLKN IWTAPLPPET ELSRQMTTST TSIDIMGLQA AYANLHTDQE RDYFMQRYRD VISSFGGKTS YDADNRPLLV MR SNFWASG YDVDGTDQTS LGQFSGRVQQ TYKHSVPRFF VPEHGTMFTL ALVRFPPTAT KEIQYLNAKG ALTYTDIAGD PAL YGNLPP REISMKDVFR SGDASKKFKI AEGQWYRYAP SYVSPAYHLL EGFPFIQEPP SGDLQERVLI RHHDYDQCFQ SVQL LQWNS QVKFNVTVYR NLPTTRDSIM TS

UniProtKB: Capsid protein F

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Macromolecule #2: Major spike protein G

MacromoleculeName: Major spike protein G / type: protein_or_peptide / ID: 2 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Microviridae (isometric ssDNA phages) / Strain: PJNS001
Molecular weightTheoretical: 19.112695 KDa
SequenceString:
MFQTFISRHN SNFFSDKLVA TSVTPASLAP VLQTPKAASS TLYFNQLTVN AGNGGFLHCI QMDTSVNAAN QVVSVGADIA FDADPKFFA CLVRFESASV PTTLPTDYDV YPLDGRHDGG YYTVKDCVTI DVLPREPGNN VYVGFMVWSN FTATKCRGLV S LNQVIKEI ICLQPLK

UniProtKB: Major spike protein G

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Macromolecule #3: DNA-binding protein J

MacromoleculeName: DNA-binding protein J / type: protein_or_peptide / ID: 3 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Microviridae (isometric ssDNA phages) / Strain: PJNS001
Molecular weightTheoretical: 4.239017 KDa
SequenceString:
MSKGKKRSGA RPGRPQPLRG TKGKRKGARL WYVGGQQF

UniProtKB: DNA-binding protein J

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
137.0 mmol/LNaClsodium chloride
2.65 mmol/LKClpotassium chloride
10.0 mmol/LNa2HPO4dibasic sodium phosphate
1.75 mmol/LKH2PO4potassium dihydrogen phosphate

Details: pH 7.2~7.6
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 4808 / Average exposure time: 1.25 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 0.4 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 22500
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

Particle selectionNumber selected: 711275
CTF correctionSoftware - Name: cryoSPARC (ver. 4.0.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0.1) / Number images used: 16905
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.0.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 15.89
Output model

PDB-9k3m:
The structure of Microviridae PJNS001

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