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- PDB-36cq: Structure of the PhiX174 bacteriophage -

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Basic information

Entry
Database: PDB / ID: 36cq
TitleStructure of the PhiX174 bacteriophage
Components
  • Capsid protein F
  • DNA-binding protein J
  • Major spike protein G
KeywordsVIRUS / Phage / Microviridae / Icosahedral / Bacteriophage
Function / homology
Function and homology information


T=1 icosahedral viral capsid / viral capsid / symbiont entry into host cell / host cell cytoplasm / 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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsLi, D.B. / King, S.H. / Driscoll, C.L. / Wilkinson, M.E. / Hie, B.L.
Funding support1items
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, 2026Deposition site: RCSB / Processing site: RCSB
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-binding protein J
B: Capsid protein F
C: Major spike protein G


Theoretical massNumber of molelcules
Total (without water)71,8373
Polymers71,8373
Non-polymers00
Water00
1
A: DNA-binding protein J
B: Capsid protein F
C: Major spike protein G
x 60


Theoretical massNumber of molelcules
Total (without water)4,310,231180
Polymers4,310,231180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein/peptide DNA-binding protein J / J protein / Small core protein


Mass: 4239.017 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinsheimervirus / Production host: Escherichia coli C (bacteria) / References: UniProt: P69592
#2: Protein Capsid protein F / F protein / GPF


Mass: 48535.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinsheimervirus / Production host: Escherichia coli C (bacteria) / References: UniProt: P03641
#3: Protein Major spike protein G / G protein / GPG


Mass: 19062.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinsheimervirus / Gene: F652_4308 / Production host: Escherichia coli C (bacteria) / References: UniProt: A3FJA7
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Sinsheimervirus / Type: VIRUS / Details: Purified from E. coli culture / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Sinsheimervirus / Strain: PhiX174
Source (recombinant)Organism: Escherichia coli C (bacteria)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMsodium chlorideNaCl1
220 mMTris1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 150000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 41.15 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.2particle selection
4cryoSPARC4.6.2CTF correction
7Coot0.9.8.96model fitting
8ISOLDE1.9model fitting
10cryoSPARCcryoSPARCinitial Euler assignment
11cryoSPARCcryoSPARCfinal Euler assignment
13cryoSPARC4.6.23D reconstruction
14RELION53D reconstruction
15PHENIX2.0_5936model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 91377 / Details: Circular blob picked
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24547 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 40.31 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00925130
ELECTRON MICROSCOPYf_angle_d0.85476981
ELECTRON MICROSCOPYf_chiral_restr0.0585761
ELECTRON MICROSCOPYf_plane_restr0.0093911
ELECTRON MICROSCOPYf_dihedral_angle_d12.40611862

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