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- PDB-9teq: PhiC31 integraseS12A-attB-RDF complex: B-bound subregion -

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Basic information

Entry
Database: PDB / ID: 9teq
TitlePhiC31 integraseS12A-attB-RDF complex: B-bound subregion
Components
  • Integrase
  • Recombination directionality factor
  • attB53_Fw
  • attB53_Rv
KeywordsRECOMBINATION / Serine integrase / Recombinase / Site-specific recombination / RDF / DNA
Function / homology
Function and homology information


provirus excision / DNA strand exchange activity / DNA binding
Similarity search - Function
Recombination directionality factor-like / Recombination directionality factor-like / DNA-binding recombinase domain / DNA-binding recombinase domain superfamily / DNA-binding recombinase domain profile. / : / Resolvase, N-terminal catalytic domain / Resolvase-like, N-terminal catalytic domain superfamily / Resolvase, N terminal domain / Resolvase, N terminal domain
Similarity search - Domain/homology
DNA / DNA (> 10) / Recombination directionality factor / Integrase
Similarity search - Component
Biological speciesLomovskayavirus C31
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsSun, Y.E. / Spagnolo, L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/W017571/1 United Kingdom
CitationJournal: To Be Published
Title: Structural mechanisms of unidirectional prophage integration and excision by serine integrases
Authors: Sun, Y.E. / Aspinall, L. / Joseph, A.P. / Colloms, S.D. / Stark, W.M. / Spagnolo, L.
History
DepositionNov 25, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 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

Downloads & links

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Assembly

Deposited unit
A: Integrase
E: attB53_Fw
F: attB53_Rv
I: Recombination directionality factor
B: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,6077
Polymers202,4765
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Integrase


Mass: 69566.398 Da / Num. of mol.: 2 / Mutation: S12A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lomovskayavirus C31 / Gene: int / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9T221
#2: DNA chain attB53_Fw


Mass: 16314.347 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lomovskayavirus C31
#3: DNA chain attB53_Rv


Mass: 16359.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lomovskayavirus C31
#4: Protein Recombination directionality factor / RDF / Gene product 3 / gp3


Mass: 30669.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lomovskayavirus C31 / Gene: 3, rdf / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9T216
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: integraseS12A-attB-RDF complex: B-bound subregion / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 0.135 MDa / Experimental value: NO
Source (natural)Organism: Lomovskayavirus C31
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 700 nm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.779 sec. / Electron dose: 49.68 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 27020
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2PHENIX1.21.2_5419model refinement
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 8561457
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60721 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 148.78 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00299284
ELECTRON MICROSCOPYf_angle_d0.614812785
ELECTRON MICROSCOPYf_chiral_restr0.03941386
ELECTRON MICROSCOPYf_plane_restr0.00681490
ELECTRON MICROSCOPYf_dihedral_angle_d20.78141703

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