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- EMDB-77391: Structure of the Evo-Phi36 bacteriophage -

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Basic information

Entry
Database: EMDB / ID: EMD-77391
TitleStructure of the Evo-Phi36 bacteriophage
Map dataStructure of the Evo-Phi36 bacteriophage
Sample
  • Virus: synthetic construct (others)
    • Protein or peptide: DNA-binding protein J
    • Protein or peptide: Capsid protein F
    • Protein or peptide: Major spike protein G
KeywordsPhage / AI / Icosahedral / Evo / VIRUS
Biological speciesSinsheimervirus / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsLi DB / King SH / Driscoll CL / Wilkinson ME / Hie BL
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Science / Year: 2026
Title: Generative design of bacteriophages with genome language models.
Authors: Samuel H King / Claudia L Driscoll / David B Li / Daniel Guo / Aditi T Merchant / Garyk Brixi / Max E Wilkinson / Brian L Hie /
Abstract: Many important biological functions arise not from single genes but from complex interactions encoded by entire genomes. We report the first generative design of complete bacteriophage genomes using ...Many important biological functions arise not from single genes but from complex interactions encoded by entire genomes. We report the first generative design of complete bacteriophage genomes using genome language models. We generated viable bacteriophages with target host tropism, using the phage ΦX174 as our design template. Experimental testing yielded 16 phages with diverse fitness profiles in laboratory conditions. Cryo-electron microscopy confirmed that a generated phage utilizes an evolutionarily distant DNA packaging protein in its capsid. A cocktail of generated phages rapidly overcomes ΦX174-resistant strains, demonstrating a path toward artificial intelligence-generated phage therapies against rapidly evolving bacterial pathogens. This work provides a blueprint for the design of diverse synthetic bacteriophages and useful biological systems at the genome scale.
History
DepositionJun 1, 2026-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77391.png

Downloads & links

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Map

FileDownload / File: emd_77391.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the Evo-Phi36 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: 0.02
Minimum - Maximum-0.027022159 - 0.08870385
Average (Standard dev.)0.00033504216 (±0.00592568)
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_77391_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_77391_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 : synthetic construct

EntireName: synthetic construct (others)
Components
  • Virus: synthetic construct (others)
    • 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: synthetic construct

SupramoleculeName: synthetic construct / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Purified from E. coli culture / NCBI-ID: 32630 / Sci species name: synthetic construct / Sci species strain: Evo-Phi36 / 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: 2.822318 KDa
Recombinant expressionOrganism: Escherichia coli C (bacteria)
SequenceString:
MKKSIRRSGG KSKGARLWYV GGTQY

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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: 48.543477 KDa
Recombinant expressionOrganism: Escherichia coli C (bacteria)
SequenceString: MSNVQTGAER MPHDLSHLGF LAGQIGRLIT ISTTPVIAGD SFEMDAVGAL RLSPLRRGLA IDSTVDIFTF YVPHRHVYGE QWIQFMKDG VNASPLPTVN TTGYIDHAAF LGTINPDTNK IPKHLFQGYL NIYNNYFKAP WMPDRTEANP NELNQDDARY G FRCCHLKN ...String:
MSNVQTGAER MPHDLSHLGF LAGQIGRLIT ISTTPVIAGD SFEMDAVGAL RLSPLRRGLA IDSTVDIFTF YVPHRHVYGE QWIQFMKDG VNASPLPTVN TTGYIDHAAF LGTINPDTNK IPKHLFQGYL NIYNNYFKAP WMPDRTEANP NELNQDDARY G FRCCHLKN IWTAPLPPET ELSRQMTTST TSIDIMGLQA AYANLHTDQE RDYFMQRYRD VISSFGGKTS YDADNRPLLV MR SNFWASG YDVDGTDQTS LGQFSGRVQQ TYKHSVPRFF VPEHGTMFTL ALVRFPPTAT KEIQYLNAKG ALTYTDIAGD PAL YGNLPP REISMKDVFR SGDASKKFKI AEGQWYRYAP SYVSPVYHLL EGFPFIQEPP SGDLQERVLI RHHDYDQCFQ SVQL LQWNS QVKFNVTVYR NLPTTRDSIM TS

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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: 19.046637 KDa
Recombinant expressionOrganism: Escherichia coli C (bacteria)
SequenceString:
MFQTFISRHN SNFFSDKLVA SSVTPASLAP VLQTPKATSS TLYFDSLTVN AANGGFLHCI QMDTSVNAAN QVVSVGADIA FDADPKFFA CLVRFESSSV PTTLPTAYDV YPLDGRHDGG YYTVKDCVTI DVLPRTPGNN VYVGFMVWSN FTATKCRGLV S LNQVIKEI ICLQPLK

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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: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 150000

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Image processing

Particle selectionNumber selected: 309522 / 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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: cryoSPARC (ver. 4.6.2), RELION (ver. 5.0)) / Number images used: 29708
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.6.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-36cr:
Structure of the Evo-Phi36 bacteriophage

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