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- EMDB-65978: Cryo-EM structure of the IS621 recombinase in complex with bridge... -

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Basic information

Entry
Database: EMDB / ID: EMD-65978
TitleCryo-EM structure of the IS621 recombinase in complex with bridge RNA, left-half DNA, and right-half DNA in the pre-strand exchange state
Map data
Sample
  • Complex: Cryo-EM structure of the IS621 recombinase in complex with bridge RNA, left-half DNA, and right-half DNA in the pre-strand exchange state
    • Protein or peptide: IS621 transposase
    • RNA: bridge RNA
    • DNA: LH, top strand
    • DNA: LH, bottom strand
    • DNA: RH, top strand
    • DNA: RH, bottom strand
  • Ligand: MAGNESIUM ION
  • Ligand: water
KeywordsHolliday junction / RNA dependent recombinase / RECOMBINATION-DNA-RNA complex / DNA BINDING PROTEIN
Function / homologyTransposase, IS111A/IS1328/IS1533, N-terminal / : / Transposase / Transposase, IS116/IS110/IS902 / Transposase IS116/IS110/IS902 family / transposase activity / DNA transposition / DNA binding / IS621 transposase
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsHiraizumi M / Tsujimoto E / Shiojiri N / Nagahata N / Yamashita K / Nishimasu H
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR23B6 Japan
Other privateInamori Foundation
CitationJournal: To Be Published
Title: Cryo-EM structure of the IS621 recombinase in complex with bridge RNA, left-half DNA, and right-half DNA in the pre-strand exchange state
Authors: Hiraizumi M
History
DepositionAug 27, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65978.png

Downloads & links

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Map

FileDownload / File: emd_65978.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 208 pix.
= 172.64 Å		0.83 Å/pix.
x 208 pix.
= 172.64 Å		0.83 Å/pix.
x 208 pix.
= 172.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.0704405 - 0.25618076
Average (Standard dev.)-0.00028353574 (±0.01274128)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin565656
Dimensions208208208
Spacing208208208
CellA=B=C: 172.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65978_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65978_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_65978_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 : Cryo-EM structure of the IS621 recombinase in complex with bridge...

EntireName: Cryo-EM structure of the IS621 recombinase in complex with bridge RNA, left-half DNA, and right-half DNA in the pre-strand exchange state
Components
  • Complex: Cryo-EM structure of the IS621 recombinase in complex with bridge RNA, left-half DNA, and right-half DNA in the pre-strand exchange state
    • Protein or peptide: IS621 transposase
    • RNA: bridge RNA
    • DNA: LH, top strand
    • DNA: LH, bottom strand
    • DNA: RH, top strand
    • DNA: RH, bottom strand
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: Cryo-EM structure of the IS621 recombinase in complex with bridge...

SupramoleculeName: Cryo-EM structure of the IS621 recombinase in complex with bridge RNA, left-half DNA, and right-half DNA in the pre-strand exchange state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: IS621 transposase

MacromoleculeName: IS621 transposase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 36.735355 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPMEHELHYI GIDTAKEKLD VDVLRPDGRH RTKKFANTTK GHDELVSWLK GHKIDHAHIC IEATGTYMEP VAECLYDAGY IVSVINPAL GKAFAQSEGL RNKTDTVDAR MLAEFCRQKR PAAWEAPHPL ERALRALVVR HQALTDMHTQ ELNRTETARE V QRPSIDAH ...String:
GPMEHELHYI GIDTAKEKLD VDVLRPDGRH RTKKFANTTK GHDELVSWLK GHKIDHAHIC IEATGTYMEP VAECLYDAGY IVSVINPAL GKAFAQSEGL RNKTDTVDAR MLAEFCRQKR PAAWEAPHPL ERALRALVVR HQALTDMHTQ ELNRTETARE V QRPSIDAH LLWLEAELKR LEKQIKDLTD DDPDMKHRRK LLESIPGIGE KTSAVLLAYI GLKDRFAHAR QFAAFAGLTP RR YESGSSV RGASRMSKAG HVSLRRALYM PAMVATSKTE WGRAFRDRLA ANGKKGKVIL GAMMRKLAQV AYGVLKSGVP FDA SRHNPV AA

UniProtKB: IS621 transposase

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Macromolecule #2: bridge RNA

MacromoleculeName: bridge RNA / type: rna / ID: 2 / Details: cell-free synthesis / Number of copies: 2
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 57.668918 KDa
SequenceString:
GGGAGUGCAG AGAAAAUCGG CCAGUUUUCU CUGCCUGCAG UCCGCAUGCC GUAUCGGGCC UUGGGUUCUA ACCUGUUCUG UAGAUUUAU GCAGCGGACU GCCUUUCUCC CAAAGUGAUA AACCGGACAG UAUCAUGGAC CGGUUUUCCC GGUAAUCCGU A UUUACAAG GCUGGUUUCA CU

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Macromolecule #3: LH, top strand

MacromoleculeName: LH, top strand / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 11.551417 KDa
SequenceString:
(DG)(DC)(DC)(DG)(DG)(DG)(DT)(DA)(DA)(DT) (DA)(DC)(DC)(DA)(DC)(DC)(DA)(DA)(DG)(DC) (DC)(DG)(DC)(DC)(DT)(DT)(DG)(DT)(DA) (DT)(DT)(DA)(DT)(DC)(DC)(DC)(DT)(DC)

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Macromolecule #4: LH, bottom strand

MacromoleculeName: LH, bottom strand / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 11.809589 KDa
SequenceString:
(DG)(DA)(DG)(DG)(DG)(DA)(DT)(DA)(DA)(DT) (DA)(DC)(DA)(DA)(DG)(DG)(DC)(DC)(DC)(DG) (DA)(DT)(DG)(DG)(DT)(DG)(DG)(DT)(DA) (DT)(DT)(DA)(DC)(DC)(DC)(DG)(DG)(DC)

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Macromolecule #5: RH, top strand

MacromoleculeName: RH, top strand / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.536707 KDa
SequenceString:
(DT)(DG)(DC)(DA)(DG)(DG)(DC)(DC)(DA)(DT) (DA)(DA)(DG)(DT)(DC)(DA)(DA)(DT)(DC)(DT) (DA)(DC)(DA)(DG)(DA)(DT)(DG)(DA)(DG) (DC)(DT)(DC)(DG)(DC)(DC)(DC)(DC)(DA)(DA) (DC) (DG)(DA)(DG)(DG)

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Macromolecule #6: RH, bottom strand

MacromoleculeName: RH, bottom strand / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.562671 KDa
SequenceString:
(DC)(DC)(DT)(DC)(DG)(DT)(DT)(DG)(DG)(DG) (DG)(DC)(DG)(DA)(DG)(DC)(DT)(DC)(DA)(DT) (DC)(DT)(DG)(DT)(DA)(DG)(DA)(DT)(DA) (DC)(DT)(DG)(DT)(DT)(DA)(DT)(DG)(DG)(DC) (DC) (DT)(DG)(DC)(DA)

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / 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: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 558374
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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