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- EMDB-77390: Structure of the PhiX174 bacteriophage -

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Basic information

Entry
Database: EMDB / ID: EMD-77390
TitleStructure of the PhiX174 bacteriophage
Map dataStructure of the PhiX174 bacteriophage
Sample
  • Virus: Sinsheimervirus
    • Protein or peptide: DNA-binding protein J
    • Protein or peptide: Capsid protein F
    • Protein or peptide: Major spike protein G
KeywordsPhage / Microviridae / Icosahedral / Bacteriophage / VIRUS
Function / homology
Function and homology information


T=1 icosahedral viral capsid / viral capsid / host cell cytoplasm / symbiont entry into host cell / structural molecule activity / DNA binding
Similarity search - Function
Microvirus J protein-like / Microvirus J protein / Microviridae F protein / Microviridae F protein superfamily / Capsid protein (F protein) / Capsid/spike protein, ssDNA virus
Similarity search - Domain/homology
: / Capsid protein F / DNA-binding protein J
Similarity search - Component
Biological speciesSinsheimervirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsLi DB / King SH / Driscoll CL / Wilkinson ME / Hie BL
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Generative design of novel bacteriophages with genome language models
Authors: King SH / Driscoll CL / Li DB / Guo D / Merchant AT / Brixi G / Wilkinson ME / Hie BL
History
DepositionJun 1, 2026-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77390.png

Downloads & links

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Map

FileDownload / File: emd_77390.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the PhiX174 bacteriophage
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 512 pix.
= 472.576 Å		0.92 Å/pix.
x 512 pix.
= 472.576 Å		0.92 Å/pix.
x 512 pix.
= 472.576 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.923 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.03566774 - 0.11276686
Average (Standard dev.)0.00041453916 (±0.007959928)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 472.576 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_77390_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_77390_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Sinsheimervirus

EntireName: Sinsheimervirus
Components
  • Virus: Sinsheimervirus
    • Protein or peptide: DNA-binding protein J
    • Protein or peptide: Capsid protein F
    • Protein or peptide: Major spike protein G

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Supramolecule #1: Sinsheimervirus

SupramoleculeName: Sinsheimervirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Purified from E. coli culture / NCBI-ID: 1910954 / Sci species name: Sinsheimervirus / Sci species strain: PhiX174 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Macromolecule #1: DNA-binding protein J

MacromoleculeName: DNA-binding protein J / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sinsheimervirus
Molecular weightTheoretical: 4.239017 KDa
Recombinant expressionOrganism: Escherichia coli C (bacteria)
SequenceString:
MSKGKKRSGA RPGRPQPLRG TKGKRKGARL WYVGGQQF

UniProtKB: DNA-binding protein J

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Macromolecule #2: Capsid protein F

MacromoleculeName: Capsid protein F / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sinsheimervirus
Molecular weightTheoretical: 48.535523 KDa
Recombinant expressionOrganism: Escherichia coli C (bacteria)
SequenceString: MSNIQTGAER MPHDLSHLGF LAGQIGRLIT ISTTPVIAGD SFEMDAVGAL RLSPLRRGLA IDSTVDIFTF YVPHRHVYGE QWIKFMKDG VNATPLPTVN TTGYIDHAAF LGTINPDTNK IPKHLFQGYL NIYNNYFKAP WMPDRTEANP NELNQDDARY G FRCCHLKN ...String:
MSNIQTGAER MPHDLSHLGF LAGQIGRLIT ISTTPVIAGD SFEMDAVGAL RLSPLRRGLA IDSTVDIFTF YVPHRHVYGE QWIKFMKDG VNATPLPTVN TTGYIDHAAF LGTINPDTNK IPKHLFQGYL NIYNNYFKAP WMPDRTEANP NELNQDDARY G FRCCHLKN IWTAPLPPET ELSRQMTTST TSIDIMGLQA AYANLHTDQE RDYFMQRYHD VISSFGGKTS YDADNRPLLV MR SNLWASG YDVDGTDQTS LGQFSGRVQQ TYKHSVPRFF VPEHGTMFTL ALVRFPPTAT KEIQYLNAKG ALTYTDIAGD PVL YGNLPP REISMKDVFR SGDSSKKFKI AEGQWYRYAP SYVSPAYHLL EGFPFIQEPP SGDLQERVLI RHHDYDQCFQ SVQL LQWNS QVKFNVTVYR NLPTTRDSIM TS

UniProtKB: Capsid protein F

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Macromolecule #3: Major spike protein G

MacromoleculeName: Major spike protein G / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sinsheimervirus
Molecular weightTheoretical: 19.062637 KDa
Recombinant expressionOrganism: Escherichia coli C (bacteria)
SequenceString:
MFQTFISRHN SNFFSDKLVL TSVTPASSAP VLQTPKATSS TLYFDSLTVN AGNGGFLHCI QMDTSVNAAN QVVSVGADIA FDADPKFFA CLVRFESSSV PTTLPTAYDV YPLDGRHDGG YYTVKDCVTI DVLPRTPGNN VYVGFMVWSN FTATKCRGLV S LNQVIKEI ICLQPLK

UniProtKB: UNIPROTKB: A3FJA7

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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: 7.4
Component:
ConcentrationFormulaName
100.0 mMNaClsodium chloride
20.0 mMTris
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 41.15 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 150000

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Image processing

Particle selectionNumber selected: 91377 / Details: Circular blob picked
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: cryoSPARC (ver. 4.6.2), RELION (ver. 5.0)) / Number images used: 24547
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. cryoSPARC)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. cryoSPARC)
FSC plot (resolution estimation)

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