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- PDB-9ifc: PhiC31 integrative synapse: CC dimer subregion -

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Basic information

Entry
Database: PDB / ID: 9ifc
TitlePhiC31 integrative synapse: CC dimer subregion
Components
  • Integrase
  • attP_Fw
  • attP_Rv
KeywordsDNA BINDING PROTEIN / Serine integrase / Recombinase / Site-specific DNA recombination / Bacteriophage
Function / homology
Function and homology information


DNA strand exchange activity / DNA binding
Similarity search - Function
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) / Integrase
Similarity search - Component
Biological speciesLomovskayavirus C31
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.79 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
DepositionFeb 18, 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
B: Integrase
E: attP_Fw
F: attP_Rv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,8435
Polymers175,7784
Non-polymers651
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: 69394.219 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 attP_Fw


Mass: 18667.889 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lomovskayavirus C31
#3: DNA chain attP_Rv


Mass: 18321.736 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lomovskayavirus C31
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / 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: PhiC31 integrative synapse: cc dimer subregion / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.1 MDa / Experimental value: NO
Source (natural)Organism: Lomovskayavirus C31
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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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 defocus max: 2300 nm / Nominal defocus min: 700 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 12.8 sec. / Electron dose: 59.8 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10330
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2PHENIX1.21.2_5419model refinement
3EPUimage acquisition
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 6090789
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.79 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29776 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 129.71 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00555289
ELECTRON MICROSCOPYf_angle_d0.66117406
ELECTRON MICROSCOPYf_chiral_restr0.0441802
ELECTRON MICROSCOPYf_plane_restr0.0043757
ELECTRON MICROSCOPYf_dihedral_angle_d24.30791196

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