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Yorodumi- PDB-8wt7: Cryo-EM structure of the IS621 recombinase in complex with bridge... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8wt7 | |||||||||
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Title | Cryo-EM structure of the IS621 recombinase in complex with bridge RNA, donor DNA, and target DNA in the pre-strand exchange locked state | |||||||||
Components |
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Keywords | RECOMBINATION/RNA/DNA / Holliday junction / RNA dependent recombinase / RECOMBINATION / RECOMBINATION-RNA-DNA complex | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Hiraizumi, M. / Yamashita, K. / Nishimasu, H. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Nature / Year: 2024 Title: Structural mechanism of bridge RNA-guided recombination Authors: Hiraizumi, M. / Perry, N.T. / Durrant, M.G. / Soma, T. / Nagahata, N. / Okazaki, S. / Athukoralage, J.S. / Isayama, Y. / Pai, J.J. / Pawluk, A. / Konermann, S. / Yamashita, K. / Hsu, P.D. / Nishimasu, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wt7.cif.gz | 382.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wt7.ent.gz | 296.8 KB | Display | PDB format |
PDBx/mmJSON format | 8wt7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wt7_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8wt7_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8wt7_validation.xml.gz | 45.8 KB | Display | |
Data in CIF | 8wt7_validation.cif.gz | 73.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/8wt7 ftp://data.pdbj.org/pub/pdb/validation_reports/wt/8wt7 | HTTPS FTP |
-Related structure data
Related structure data | 37828MC 8wt6C 8wt8C 8wt9C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-DNA chain , 4 types, 4 molecules GHIJ
#3: DNA chain | Mass: 11659.493 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The linkage between 25G and 26G has been cleaved by IS621. Source: (synth.) Escherichia coli (E. coli) |
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#4: DNA chain | Mass: 11703.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
#5: DNA chain | Mass: 13507.688 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The linkage between 20I and 21I has been cleaved by IS621. Source: (synth.) Escherichia coli (E. coli) |
#6: DNA chain | Mass: 13587.737 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
-Protein / RNA chain , 2 types, 6 molecules ABCDEF
#1: Protein | Mass: 36735.355 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: O3K_03330, O3K_03970, O3K_05990, O3K_07835, O3K_09380, O3K_16710, O3K_17245, O3K_20600, O3K_22425 Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A0E0Y1P1 #2: RNA chain | Mass: 57668.918 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: synthetic construct (others) |
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-Non-polymers , 2 types, 6 molecules
#7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: The IS621 recombinase in complex with bridge RNA, donor DNA, and target DNA in the pre-strand exchange locked state Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 49.3 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 875289 / Symmetry type: POINT |