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- EMDB-72632: attPsym bound large serine integrase and RDF complex in the dimer... -

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Basic information

Entry
Database: EMDB / ID: EMD-72632
TitleattPsym bound large serine integrase and RDF complex in the dimeric state
Map datasharpened map
Sample
  • Complex: attPsym bound dimeric complex of large serine integrase and RDF fusion proteins.
    • Protein or peptide: Resolvase homolog YokA,SPbeta prophage-derived uncharacterized protein YotN
    • DNA: attPsym
  • DNA: attPsym
  • Ligand: ZINC ION
KeywordsSite-specific DNA Recombinase / Large serine integrase / DNA binding domains / Recombinase / Resolvase / Zinc ribbon recombinase / RECOMBINATION
Function / homology
Function and homology information


DNA strand exchange activity / DNA integration / DNA recombination / DNA binding
Similarity search - Function
Recombinase / DNA-binding recombinase domain / DNA-binding recombinase domain superfamily / DNA-binding recombinase domain profile. / : / Resolvase/invertase-type recombinase catalytic 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
Resolvase homolog YokA / SPbeta prophage-derived uncharacterized protein YotN
Similarity search - Component
Biological speciesSpbetavirus SPbeta
Methodsingle particle reconstruction / cryo EM / Resolution: 7.1 Å
AuthorsShin H / Olorunniji FJ / Rice PA
Funding support United States, United Kingdom, 3 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2223480 United States
UK Research and Innovation (UKRI)2223480 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)2223480 United Kingdom
CitationJournal: bioRxiv / Year: 2025
Title: Structural basis of directionality control in large serine integrases.
Authors: Heewhan Shin / Ying Pigli / Tania Peña Reyes / James R Fuller / Femi J Olorunniji / Phoebe A Rice /
Abstract: Large serine integrases (LSIs) catalyze unidirectional site-specific DNA recombination reactions, yet those reactions are reversed by the presence of a cognate recombination directionality factor ...Large serine integrases (LSIs) catalyze unidirectional site-specific DNA recombination reactions, yet those reactions are reversed by the presence of a cognate recombination directionality factor (RDF). Mechanistic understanding of directionality control has been hampered by a lack of structural information. Here, we use cryo-electron microscopy (cryo-EM) to determine the structures of six SPbeta integrase-DNA complexes along the integrative (-RDF) and excisive (+RDF) reaction pathways, at 4.16-7.18Å resolution. Our findings reveal how RDF-mediated repositioning of an integrase subdomain (1) dictates which pairs of DNA sites can be assembled into a synaptic complex to initiate recombination and (2) dictates which product complexes will be conformationally locked, preventing the back reaction. These mechanistic insights provide a conceptual framework for engineering efficient and versatile genome editing tools.
History
DepositionSep 9, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72632.png

Downloads & links

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Map

FileDownload / File: emd_72632.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 320 pix.
= 340.8 Å		1.07 Å/pix.
x 320 pix.
= 340.8 Å		1.07 Å/pix.
x 320 pix.
= 340.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.597358 - 1.0504786
Average (Standard dev.)0.0011644525 (±0.022397876)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 340.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened map

Fileemd_72632_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_72632_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_72632_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : attPsym bound dimeric complex of large serine integrase and RDF f...

EntireName: attPsym bound dimeric complex of large serine integrase and RDF fusion proteins.
Components
  • Complex: attPsym bound dimeric complex of large serine integrase and RDF fusion proteins.
    • Protein or peptide: Resolvase homolog YokA,SPbeta prophage-derived uncharacterized protein YotN
    • DNA: attPsym
  • DNA: attPsym
  • Ligand: ZINC ION

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Supramolecule #1: attPsym bound dimeric complex of large serine integrase and RDF f...

SupramoleculeName: attPsym bound dimeric complex of large serine integrase and RDF fusion proteins.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Spbetavirus SPbeta

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Macromolecule #1: Resolvase homolog YokA,SPbeta prophage-derived uncharacterized pr...

MacromoleculeName: Resolvase homolog YokA,SPbeta prophage-derived uncharacterized protein YotN
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Spbetavirus SPbeta
Molecular weightTheoretical: 71.56018 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MELKNIVNSY NITNILGYLR RSRQDMEREK RTGEDTLTEQ KELMNKILTA IEIPYELKME IGSGESIDGR PVFKECLKDL EEGKYQAIA VKEITRLSRG SYSDAGQIVN LLQSKRLIII TPYKVYDPRN PVDMRQIRFE LFMAREEFEM TRERMTGAKY T YAAQGKWI ...String:
MELKNIVNSY NITNILGYLR RSRQDMEREK RTGEDTLTEQ KELMNKILTA IEIPYELKME IGSGESIDGR PVFKECLKDL EEGKYQAIA VKEITRLSRG SYSDAGQIVN LLQSKRLIII TPYKVYDPRN PVDMRQIRFE LFMAREEFEM TRERMTGAKY T YAAQGKWI SGLAPYGYQL NKKTSKLDPV EDEAKVVQLI FNIFLNGLNG KDYSYTAIAS HLTNLQIPTP SGKKRWNQYT IK AILQNEV YIGTVKYKVR EKTKDGKRTI RPEKEQIVVQ DAHAPIIDKE QFQQSQVKIA NKVPLLPNKD EFELSELAGV CTC SKCGEP LSKYESKRIR KNKDGTESVY HVKSLTCKKN KCTYVRYNDV ENAILDYLSS LNDLNDSTLT KHINSMLSKY EDDN SNMKT KKQMSEHLSQ KEKELKNKEN FIFDKYESGI YSDELFLKRK AALDEEFKEL QNAKNELNGL QDTQSEIDSN TVRNN INKI IDQYHIESSS EKKNELLRMV LKDVIVNMTQ KRKGPIPAQF EITPILRFNF IFDLTATNSF HTSGSGGSGG SGGSGR SGT EPYQRYEELK KKTIKVVQKE NYSIRYITQD EASNDLDEFY KQFAQHLLEA ALERKAE

UniProtKB: Resolvase homolog YokA, SPbeta prophage-derived uncharacterized protein YotN

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Macromolecule #2: attPsym

MacromoleculeName: attPsym / type: dna / ID: 2 / Details: DNA duplex / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Spbetavirus SPbeta
Molecular weightTheoretical: 20.761484 KDa
SequenceString: (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DG)(DG)(DT)(DA)(DG)(DT)(DA)(DA)(DG) (DT)(DA)(DT)(DC)(DT)(DT)(DA)(DA)(DA) (DA)(DA)(DA)(DC)(DA)(DG)(DA)(DT)(DA)(DT) (DA) (DG)(DC)(DT)(DG)(DT)(DA) ...String:
(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DG)(DG)(DT)(DA)(DG)(DT)(DA)(DA)(DG) (DT)(DA)(DT)(DC)(DT)(DT)(DA)(DA)(DA) (DA)(DA)(DA)(DC)(DA)(DG)(DA)(DT)(DA)(DT) (DA) (DG)(DC)(DT)(DG)(DT)(DA)(DT)(DA) (DT)(DT)(DA)(DA)(DG)(DA)(DT)(DA)(DC)(DT) (DT)(DA) (DC)(DT)(DA)(DC)(DA)(DT)(DA)

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Macromolecule #3: attPsym

MacromoleculeName: attPsym / type: dna / ID: 3 / Details: DNA duplex / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Spbetavirus SPbeta
Molecular weightTheoretical: 20.528189 KDa
SequenceString: (DT)(DA)(DT)(DG)(DT)(DA)(DG)(DT)(DA)(DA) (DG)(DT)(DA)(DT)(DC)(DT)(DT)(DA)(DA)(DT) (DA)(DT)(DA)(DC)(DA)(DG)(DC)(DT)(DA) (DT)(DA)(DT)(DC)(DT)(DG)(DT)(DT)(DT)(DT) (DT) (DT)(DA)(DA)(DG)(DA)(DT) ...String:
(DT)(DA)(DT)(DG)(DT)(DA)(DG)(DT)(DA)(DA) (DG)(DT)(DA)(DT)(DC)(DT)(DT)(DA)(DA)(DT) (DA)(DT)(DA)(DC)(DA)(DG)(DC)(DT)(DA) (DT)(DA)(DT)(DC)(DT)(DG)(DT)(DT)(DT)(DT) (DT) (DT)(DA)(DA)(DG)(DA)(DT)(DA)(DC) (DT)(DT)(DA)(DC)(DT)(DA)(DC)(DC)(DT)(DT) (DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Details: DNA duplex / 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: 8
Component:
ConcentrationFormulaName
100.0 mMNaClsodium chloride
20.0 mMC4H11NO3Tris

Details: 20mM Tris-HCl, 100mM NaCl
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291.15 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 24616
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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