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- EMDB-55831: PhiC31 excisive synapse: P'-bound subregion -

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Basic information

Entry
Database: EMDB / ID: EMD-55831
TitlePhiC31 excisive synapse: P'-bound subregion
Map data
Sample
  • Complex: PhiC31 excisive synapse: P'-bound subregion
    • Protein or peptide: Integrase
    • DNA: attL60_Fw
    • DNA: attL60_Rv
    • Protein or peptide: Recombination directionality factor
  • Ligand: ZINC ION
KeywordsSerine integrase / Recombinase / Site-specific recombination / RDF / DNA / RECOMBINATION
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
Recombination directionality factor / Integrase
Similarity search - Component
Biological speciesLomovskayavirus C31
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsSun YE / Spagnolo L
Funding support United Kingdom, 1 items
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 YE / Aspinall L / Joseph AP / Colloms SD / Stark WM / Spagnolo L
History
DepositionNov 25, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55831.png

Downloads & links

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Map

FileDownload / File: emd_55831.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 360 pix.
= 381.6 Å		1.06 Å/pix.
x 360 pix.
= 381.6 Å		1.06 Å/pix.
x 360 pix.
= 381.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.017241186 - 0.05824343
Average (Standard dev.)0.000034833152 (±0.0010387019)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 381.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55831_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55831_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55831_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PhiC31 excisive synapse: P'-bound subregion

EntireName: PhiC31 excisive synapse: P'-bound subregion
Components
  • Complex: PhiC31 excisive synapse: P'-bound subregion
    • Protein or peptide: Integrase
    • DNA: attL60_Fw
    • DNA: attL60_Rv
    • Protein or peptide: Recombination directionality factor
  • Ligand: ZINC ION

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Supramolecule #1: PhiC31 excisive synapse: P'-bound subregion

SupramoleculeName: PhiC31 excisive synapse: P'-bound subregion / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Lomovskayavirus C31
Molecular weightTheoretical: 117 KDa

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Macromolecule #1: Integrase

MacromoleculeName: Integrase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Lomovskayavirus C31
Molecular weightTheoretical: 69.566398 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MDTYAGAYDR QARERENSSA ASPATQRSAN EDKAADLQRE VERDGGRFRF VGHFSEAPGT SAFGTAERP EFERILNECR AGRLNMIIVY DVSRFSRLKV MDAIPIVSEL LALGVTIVST QEGVFRQGNV MDLIHLIMRL D ASHKESSL ...String:
MGSSHHHHHH SSGLVPRGSH MDTYAGAYDR QARERENSSA ASPATQRSAN EDKAADLQRE VERDGGRFRF VGHFSEAPGT SAFGTAERP EFERILNECR AGRLNMIIVY DVSRFSRLKV MDAIPIVSEL LALGVTIVST QEGVFRQGNV MDLIHLIMRL D ASHKESSL KSAKILDTKN LQRELGGYVG GKAPYGFELV SETKEITRNG RMVNVVINKL AHSTTPLTGP FEFEPDVIRW WW REIKTHK HLPFKPGSQA AIHPGSITGL CKRMDADAVP TRGETIGKKT ASSAWDPATV MRILRDPRIA GFAAEVIYKK KPD GTPTTK IEGYRIQRDP ITLRPVELDC GPIIEPAEWY ELQAWLDGRG RGKGLSRGQA ILSAMDKLYC ECGAVMTSKR GEES IKDSY RCRRRKVVDP SAPGQHEGTC NVSMAALDKF VAERIFNKIR HAEGDEETLA LLWEAARRFG KLTEAPEKSG ERANL VAER ADALNALEEL YEDRAAGAYD GPVGRKHFRK QQAALTLRQQ GAEERLAELE AAEAPKLPLD QWFPEDADAD PTGPKS WWG RASVDDKRVF VGLFVDKIVV TKSTTGRGQG TPIEKRASIT WAKPPTDDDE DDAQDGTEDV AATS

UniProtKB: Integrase

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Macromolecule #4: Recombination directionality factor

MacromoleculeName: Recombination directionality factor / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lomovskayavirus C31
Molecular weightTheoretical: 30.669271 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSYYHHHHHH DYDIPTTENL YFQGAMAMAK RSIWAGDEDN KPKKRETYAD DTVGRFHSGY SETNERGKVV PVALDKWRIS TGEQSVADA VAQLFGGTPV ENEESTSENF IDVFTDRPKV PVIIEADGIH WDMKLWLNGK LKHHCDGFDF VSHADEEMIG Q PCGCPKLF ...String:
MSYYHHHHHH DYDIPTTENL YFQGAMAMAK RSIWAGDEDN KPKKRETYAD DTVGRFHSGY SETNERGKVV PVALDKWRIS TGEQSVADA VAQLFGGTPV ENEESTSENF IDVFTDRPKV PVIIEADGIH WDMKLWLNGK LKHHCDGFDF VSHADEEMIG Q PCGCPKLF DERKAAAKEY DAPNPAITVT FTLADDPELG RFKFQTGSWT LFKVLHEAED DVERVGKGGA VLANLELELV EY TPKRGPM RNKLVSYYKP TITVLKSYND AIAD

UniProtKB: Recombination directionality factor

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Macromolecule #2: attL60_Fw

MacromoleculeName: attL60_Fw / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Lomovskayavirus C31
Molecular weightTheoretical: 18.701863 KDa
SequenceString: (DA)(DG)(DC)(DC)(DG)(DC)(DG)(DG)(DT)(DG) (DC)(DG)(DG)(DG)(DT)(DG)(DC)(DC)(DA)(DG) (DG)(DG)(DC)(DG)(DT)(DG)(DC)(DC)(DC) (DT)(DT)(DG)(DA)(DG)(DT)(DT)(DC)(DT)(DC) (DT) (DC)(DA)(DG)(DT)(DT)(DG) ...String:
(DA)(DG)(DC)(DC)(DG)(DC)(DG)(DG)(DT)(DG) (DC)(DG)(DG)(DG)(DT)(DG)(DC)(DC)(DA)(DG) (DG)(DG)(DC)(DG)(DT)(DG)(DC)(DC)(DC) (DT)(DT)(DG)(DA)(DG)(DT)(DT)(DC)(DT)(DC) (DT) (DC)(DA)(DG)(DT)(DT)(DG)(DG)(DG) (DG)(DG)(DC)(DG)(DT)(DA)(DG)(DG)(DG)(DT) (DC)(DG)

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Macromolecule #3: attL60_Rv

MacromoleculeName: attL60_Rv / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Lomovskayavirus C31
Molecular weightTheoretical: 18.293691 KDa
SequenceString: (DC)(DG)(DA)(DC)(DC)(DC)(DT)(DA)(DC)(DG) (DC)(DC)(DC)(DC)(DC)(DA)(DA)(DC)(DT)(DG) (DA)(DG)(DA)(DG)(DA)(DA)(DC)(DT)(DC) (DA)(DA)(DG)(DG)(DG)(DC)(DA)(DC)(DG)(DC) (DC) (DC)(DT)(DG)(DG)(DC)(DA) ...String:
(DC)(DG)(DA)(DC)(DC)(DC)(DT)(DA)(DC)(DG) (DC)(DC)(DC)(DC)(DC)(DA)(DA)(DC)(DT)(DG) (DA)(DG)(DA)(DG)(DA)(DA)(DC)(DT)(DC) (DA)(DA)(DG)(DG)(DG)(DC)(DA)(DC)(DG)(DC) (DC) (DC)(DT)(DG)(DG)(DC)(DA)(DC)(DC) (DC)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DG)(DG) (DC)(DT)

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

Concentration0.5 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 7611 / Average exposure time: 4.5 sec. / Average electron dose: 60.07 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4359047
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 66541
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9teo:
PhiC31 excisive synapse: P'-bound subregion

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