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- EMDB-37829: Cryo-EM structure of the IS621 recombinase in complex with bridge... -

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Basic information

Entry
Database: EMDB / ID: EMD-37829
TitleCryo-EM structure of the IS621 recombinase in complex with bridge RNA, donor DNA, and target DNA in the post-strand exchange state (Holliday junction intermediate)
Map data
Sample
  • Complex: The IS621 recombinase in complex with bridge RNA, donor DNA, and target DNA in the post-strand exchange state (Holliday junction intermediate)
    • Protein or peptide: IS621 transposase
    • RNA: bridge RNA
    • DNA: target DNA-donor DNA
    • DNA: target DNA
    • DNA: donor DNA-target DNA
    • DNA: donor DNA
  • Ligand: MAGNESIUM ION
KeywordsHolliday junction / RNA dependent recombinase / RECOMBINATION-RNA-DNA COMPLEX
Function / homologyTransposase, IS111A/IS1328/IS1533, N-terminal / Transposase, IS116/IS110/IS902 / : / Transposase / 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: 2.9 Å
AuthorsHiraizumi M / Yamashita K / Nishimasu H
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR23B6 Japan
Other privateInamori Foundation
CitationJournal: Nature / Year: 2024
Title: Structural mechanism of bridge RNA-guided recombination
Authors: Hiraizumi M / Perry NT / Durrant MG / Soma T / Nagahata N / Okazaki S / Athukoralage JS / Isayama Y / Pai JJ / Pawluk A / Konermann S / Yamashita K / Hsu PD / Nishimasu H
History
DepositionOct 18, 2023-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37829.png

Downloads & links

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Map

FileDownload / File: emd_37829.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.10667 Å
Density
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.34007472 - 0.84418106
Average (Standard dev.)-0.0008846668 (±0.025724959)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 265.6001 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_37829_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_37829_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_37829_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 : The IS621 recombinase in complex with bridge RNA, donor DNA, and ...

EntireName: The IS621 recombinase in complex with bridge RNA, donor DNA, and target DNA in the post-strand exchange state (Holliday junction intermediate)
Components
  • Complex: The IS621 recombinase in complex with bridge RNA, donor DNA, and target DNA in the post-strand exchange state (Holliday junction intermediate)
    • Protein or peptide: IS621 transposase
    • RNA: bridge RNA
    • DNA: target DNA-donor DNA
    • DNA: target DNA
    • DNA: donor DNA-target DNA
    • DNA: donor DNA
  • Ligand: MAGNESIUM ION

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Supramolecule #1: The IS621 recombinase in complex with bridge RNA, donor DNA, and ...

SupramoleculeName: The IS621 recombinase in complex with bridge RNA, donor DNA, and target DNA in the post-strand exchange state (Holliday junction intermediate)
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 / 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: target DNA-donor DNA

MacromoleculeName: target DNA-donor DNA / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 15.003622 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)(DC) (DA) (DG)(DT)(DG)(DC)(DA)(DG)(DA)(DG) (DA)

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Macromolecule #4: target DNA

MacromoleculeName: target DNA / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 11.703487 KDa
SequenceString:
(DC)(DG)(DA)(DG)(DC)(DT)(DC)(DA)(DT)(DC) (DT)(DG)(DT)(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: donor DNA-target DNA

MacromoleculeName: donor DNA-target DNA / type: dna / ID: 5
Details: The linkage between 20I and 21I has been cleaved by IS621.
Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 10.163561 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)

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Macromolecule #6: donor DNA

MacromoleculeName: donor DNA / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.587737 KDa
SequenceString:
(DT)(DC)(DT)(DC)(DT)(DG)(DC)(DA)(DC)(DT) (DG)(DG)(DA)(DG)(DG)(DG)(DA)(DT)(DA)(DA) (DT)(DA)(DC)(DA)(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: 1 / Formula: MG
Molecular weightTheoretical: 24.305 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 62.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 630357
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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