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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 / 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
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: To Be Published
Title: Generative design of novel bacteriophages with genome language models
Authors: King, S.H. / Driscoll, C.L. / Li, D.B. / Guo, D. / Merchant, A.T. / Brixi, G. / Wilkinson, M.E. / Hie, B.L.
History
DepositionJun 1, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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