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- EMDB-52845: PhiC31 integrative synapse: CC dimer subregion -

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Basic information

Entry
Database: EMDB / ID: EMD-52845
TitlePhiC31 integrative synapse: CC dimer subregion
Map data
Sample
  • Complex: PhiC31 integrative synapse: cc dimer subregion
    • Protein or peptide: Integrase
    • DNA: attP_Fw
    • DNA: attP_Rv
  • Ligand: ZINC ION
KeywordsSerine integrase / Recombinase / Site-specific DNA recombination / Bacteriophage / DNA BINDING PROTEIN
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
Biological speciesLomovskayavirus C31
Methodsingle particle reconstruction / cryo EM / Resolution: 3.79 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
DepositionFeb 18, 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_52845.png

Downloads & links

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Map

FileDownload / File: emd_52845.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.17 Å/pix.
x 320 pix.
= 374.72 Å		1.17 Å/pix.
x 320 pix.
= 374.72 Å		1.17 Å/pix.
x 320 pix.
= 374.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.171 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.043024797 - 0.09111294
Average (Standard dev.)0.00001604991 (±0.0016284533)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 374.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52845_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52845_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52845_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 integrative synapse: cc dimer subregion

EntireName: PhiC31 integrative synapse: cc dimer subregion
Components
  • Complex: PhiC31 integrative synapse: cc dimer subregion
    • Protein or peptide: Integrase
    • DNA: attP_Fw
    • DNA: attP_Rv
  • Ligand: ZINC ION

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Supramolecule #1: PhiC31 integrative synapse: cc dimer subregion

SupramoleculeName: PhiC31 integrative synapse: cc dimer subregion / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Lomovskayavirus C31
Molecular weightTheoretical: 100 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: 69.394219 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MDTYAGAYDR QSRERENSSA ASPATQRSAN EDKAADLQRE VERDGGRFRF VGHFSEAPGT SAFGTAERP EFERILNECR AGRLNMIIVY DVSRFSRLKV MDAIPIVSEL LALGVTIVST QEGVFRQGNV MDLIHLIMRL D ASHKESSL ...String:
MGSSHHHHHH SSGLVPRGSH MDTYAGAYDR QSRERENSSA 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 AA

UniProtKB: Integrase

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Macromolecule #2: attP_Fw

MacromoleculeName: attP_Fw / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Lomovskayavirus C31
Molecular weightTheoretical: 18.667889 KDa
SequenceString: (DC)(DG)(DG)(DG)(DA)(DG)(DT)(DA)(DG)(DT) (DG)(DC)(DC)(DC)(DC)(DA)(DA)(DC)(DT)(DG) (DG)(DG)(DG)(DT)(DA)(DA)(DC)(DC)(DT) (DT)(DT)(DG)(DA)(DG)(DT)(DT)(DC)(DT)(DC) (DT) (DC)(DA)(DG)(DT)(DT)(DG) ...String:
(DC)(DG)(DG)(DG)(DA)(DG)(DT)(DA)(DG)(DT) (DG)(DC)(DC)(DC)(DC)(DA)(DA)(DC)(DT)(DG) (DG)(DG)(DG)(DT)(DA)(DA)(DC)(DC)(DT) (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: attP_Rv

MacromoleculeName: attP_Rv / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Lomovskayavirus C31
Molecular weightTheoretical: 18.321736 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)(DA)(DG)(DG)(DT)(DT)(DA)(DC)(DC) (DC) (DC)(DA)(DG)(DT)(DT)(DG) ...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)(DA)(DG)(DG)(DT)(DT)(DA)(DC)(DC) (DC) (DC)(DA)(DG)(DT)(DT)(DG)(DG)(DG) (DG)(DC)(DA)(DC)(DT)(DA)(DC)(DT)(DC)(DC) (DC)(DG)

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / 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

BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 20 eV
SoftwareName: EPU
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 10330 / Average exposure time: 12.8 sec. / Average electron dose: 59.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.7000000000000001 µm
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: 6090789
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.79 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 29776
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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