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- EMDB-53874: PhiC31 integrase-attL complex: B-bound subregion -

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Basic information

Entry
Database: EMDB / ID: EMD-53874
TitlePhiC31 integrase-attL complex: B-bound subregion
Map datamap
Sample
  • Complex: Integrase-attL complex: B-bound subregion
    • Protein or peptide: PhiC31 integrase
    • DNA: attL_Fw
    • DNA: attL_Rv
  • Ligand: ZINC ION
KeywordsSerine integrase / Recombinase / Site-specific DNA recombination / Bacteriophage / DNA BINDING PROTEIN
Biological speciesLomovskayavirus C31
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsSpagnolo L / Sun YE / Joseph AP
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
DepositionMay 20, 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_53874.png

Downloads & links

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Map

FileDownload / File: emd_53874.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 274.432 Å		1.07 Å/pix.
x 256 pix.
= 274.432 Å		1.07 Å/pix.
x 256 pix.
= 274.432 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.072 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.018656552 - 0.046052493
Average (Standard dev.)0.000018129349 (±0.0012054569)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 274.432 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: map

Fileemd_53874_half_map_1.map
Annotationmap
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: map

Fileemd_53874_half_map_2.map
Annotationmap
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Integrase-attL complex: B-bound subregion

EntireName: Integrase-attL complex: B-bound subregion
Components
  • Complex: Integrase-attL complex: B-bound subregion
    • Protein or peptide: PhiC31 integrase
    • DNA: attL_Fw
    • DNA: attL_Rv
  • Ligand: ZINC ION

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Supramolecule #1: Integrase-attL complex: B-bound subregion

SupramoleculeName: Integrase-attL complex: B-bound subregion / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Lomovskayavirus C31
Molecular weightTheoretical: 175 KDa

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Macromolecule #1: PhiC31 integrase

MacromoleculeName: PhiC31 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

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Macromolecule #2: attL_Fw

MacromoleculeName: attL_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: attL_Rv

MacromoleculeName: attL_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 #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

Concentration0.4 mg/mL
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: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 8830 / Average exposure time: 4.1 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 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: 11870342
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 112514
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-9rad:
PhiC31 integrase-attL complex: B-bound subregion

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