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- EMDB-52841: PhiC31 S12A dimer on attB sites -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-52841
TitlePhiC31 S12A dimer on attB sites
Map data
Sample
  • Complex: PhiC31 integrase S12A on attB site
    • DNA: DNA (53-MER)
    • DNA: DNA (53-MER)
    • Protein or peptide: Integrase
  • Ligand: ZINC ION
Keywordsintegrase / PhiC31 / 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 speciesStreptomyces phage phi-C31 (virus) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 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 basis of DNA recombination catalysis and regulation by phiC31 integrase
Authors: Spagnolo L / Sun YE / Aspinall L / Joseph AP / Stark WM / Colloms SD
History
DepositionFeb 17, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52841.png

Downloads & links

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Map

FileDownload / File: emd_52841.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: 0.01
Minimum - Maximum-0.09336431 - 0.1368809
Average (Standard dev.)-0.000053594285 (±0.0019204859)
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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Additional map: #1

Fileemd_52841_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52841_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_52841_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 integrase S12A on attB site

EntireName: PhiC31 integrase S12A on attB site
Components
  • Complex: PhiC31 integrase S12A on attB site
    • DNA: DNA (53-MER)
    • DNA: DNA (53-MER)
    • Protein or peptide: Integrase
  • Ligand: ZINC ION

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Supramolecule #1: PhiC31 integrase S12A on attB site

SupramoleculeName: PhiC31 integrase S12A on attB site / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Streptomyces phage phi-C31 (virus)

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Macromolecule #1: DNA (53-MER)

MacromoleculeName: DNA (53-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 16.314347 KDa
SequenceString: (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)(DG)(DG)(DC)(DT)(DC)(DC)(DC)(DC)(DG) (DG) (DG)(DC)(DG)(DC)(DG)(DT) ...String:
(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)(DG)(DG)(DC)(DT)(DC)(DC)(DC)(DC)(DG) (DG) (DG)(DC)(DG)(DC)(DG)(DT)(DA)(DC) (DT)(DC)(DC)(DA)(DC)

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Macromolecule #2: DNA (53-MER)

MacromoleculeName: DNA (53-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 16.359412 KDa
SequenceString: (DG)(DT)(DG)(DG)(DA)(DG)(DT)(DA)(DC)(DG) (DC)(DG)(DC)(DC)(DC)(DG)(DG)(DG)(DG)(DA) (DG)(DC)(DC)(DC)(DA)(DA)(DG)(DG)(DG) (DC)(DA)(DC)(DG)(DC)(DC)(DC)(DT)(DG)(DG) (DC) (DA)(DC)(DC)(DC)(DG)(DC) ...String:
(DG)(DT)(DG)(DG)(DA)(DG)(DT)(DA)(DC)(DG) (DC)(DG)(DC)(DC)(DC)(DG)(DG)(DG)(DG)(DA) (DG)(DC)(DC)(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)

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Macromolecule #3: Integrase

MacromoleculeName: Integrase / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces phage phi-C31 (virus)
Molecular weightTheoretical: 50.003789 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DASHKESSLK SAKILDTKNL QRELGGYVGG KAPYGFELVS ETKEITRNGR MVNVVINKLA HSTTPLTGPF EFEPDVIRWW WREIKTHKH LPFKPGSQAA IHPGSITGLC KRMDADAVPT RGETIGKKTA SSAWDPATVM RILRDPRIAG FAAEVIYKKK P DGTPTTKI ...String:
DASHKESSLK SAKILDTKNL QRELGGYVGG KAPYGFELVS ETKEITRNGR MVNVVINKLA HSTTPLTGPF EFEPDVIRWW WREIKTHKH LPFKPGSQAA IHPGSITGLC KRMDADAVPT RGETIGKKTA SSAWDPATVM RILRDPRIAG FAAEVIYKKK P DGTPTTKI EGYRIQRDPI TLRPVELDCG PIIEPAEWYE LQAWLDGRGR GKGLSRGQAI LSAMDKLYCE CGAVMTSKRG EE SIKDSYR CRRRKVVDPS APGQHEGTCN VSMAALDKFV AERIFNKIRH AEGDEETLAL LWEAARRFGK LTEAPEKSGE RAN LVAERA DALNALEELY EDRAAGAYDG PVGRKHFRKQ QAALTLRQQG AEERLAELEA AEAPKLPLDQ WFPEDADADP TGPK SWWGR ASVDDKRVFV GLFVDKIVVT KSTTGRGQGT PIEKRASITW AKPPT

UniProtKB: Integrase

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / 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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 274520
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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