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- EMDB-47287: attP bound large serine integrase and RDF complex in the dimeric ... -

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Basic information

Entry
Database: EMDB / ID: EMD-47287
TitleattP bound large serine integrase and RDF complex in the dimeric state (cleaved)
Map datasharpened map
Sample
  • Complex: attLmm bound serine integrase and RDF complex in the pre-rotation state
    • Protein or peptide: Resolvase homolog YokA,SPbeta prophage-derived uncharacterized protein YotN
    • DNA: DNA (34-MER)
    • DNA: DNA (33-MER)
  • Ligand: ZINC ION
KeywordsViral protein / Integrase / Recombinase / Complex / Recombination Directionality Factor / Integration / Excision / DNA BINDING PROTEIN
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 speciesBacillus subtilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.61 Å
AuthorsShin H / Rice PA / Olorunniji FJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: To Be Published
Title: Structural Basis of Directionality Control in Large Serine Integrases
Authors: Shin HS / Rice PA
History
DepositionOct 11, 2024-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47287.png

Downloads & links

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Map

FileDownload / File: emd_47287.map.gz / Format: CCP4 / Size: 15.6 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.)
2.13 Å/pix.
x 160 pix.
= 340.8 Å		2.13 Å/pix.
x 160 pix.
= 340.8 Å		2.13 Å/pix.
x 160 pix.
= 340.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.13 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.80859345 - 1.9602631
Average (Standard dev.)0.0018006287 (±0.047679)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 340.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47287_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: raw map

Fileemd_47287_additional_1.map
Annotationraw map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half A map

Fileemd_47287_half_map_1.map
Annotationhalf A map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half B map

Fileemd_47287_half_map_2.map
Annotationhalf B 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 : attLmm bound serine integrase and RDF complex in the pre-rotation...

EntireName: attLmm bound serine integrase and RDF complex in the pre-rotation state
Components
  • Complex: attLmm bound serine integrase and RDF complex in the pre-rotation state
    • Protein or peptide: Resolvase homolog YokA,SPbeta prophage-derived uncharacterized protein YotN
    • DNA: DNA (34-MER)
    • DNA: DNA (33-MER)
  • Ligand: ZINC ION

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Supramolecule #1: attLmm bound serine integrase and RDF complex in the pre-rotation...

SupramoleculeName: attLmm bound serine integrase and RDF complex in the pre-rotation state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Bacillus subtilis (bacteria)

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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: Bacillus subtilis (bacteria)
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: DNA (34-MER)

MacromoleculeName: DNA (34-MER) / type: dna / ID: 2 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 10.433742 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(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)(DT)

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Macromolecule #3: DNA (33-MER)

MacromoleculeName: DNA (33-MER) / type: dna / ID: 3 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 10.161636 KDa
SequenceString:
(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)(DA)(DA)(DA) (DA)(DA)(DA)(DA)

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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: 8
Sugar embeddingMaterial: vitreous ice
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (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 / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.61 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 54766
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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