[English] 日本語
![](img/lk-miru.gif)
- PDB-8wt8: Cryo-EM structure of the IS621 recombinase in complex with bridge... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8wt8 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-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) | |||||||||
![]() |
| |||||||||
![]() | RECOMBINATION/RNA/DNA / Holliday junction / RNA dependent recombinase / RECOMBINATION-RNA-DNA COMPLEX | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
![]() | Hiraizumi, M. / Yamashita, K. / Nishimasu, H. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 381.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 297.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 46.7 KB | Display | |
Data in CIF | ![]() | 74.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 37829MC ![]() 8wt6C ![]() 8wt7C ![]() 8wt9C M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-DNA chain , 4 types, 4 molecules GHIJ
#3: DNA chain | Mass: 15003.622 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
---|---|
#4: DNA chain | Mass: 11703.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#5: DNA chain | Mass: 10163.561 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The linkage between 20I and 21I has been cleaved by IS621. Source: (synth.) ![]() ![]() |
#6: DNA chain | Mass: 13587.737 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
-Protein / RNA chain / Non-polymers , 3 types, 7 molecules ABCDEF![](data/chem/img/MG.gif)
![](data/chem/img/MG.gif)
#1: Protein | Mass: 36735.355 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: O3K_03330, O3K_03970, O3K_05990, O3K_07835, O3K_09380, O3K_16710, O3K_17245, O3K_20600, O3K_22425 Production host: ![]() ![]() #2: RNA chain | Mass: 57668.918 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #7: Chemical | ChemComp-MG / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
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 post-strand exchange state (Holliday junction intermediate) Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
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 |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 62 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-
Processing
EM software |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 630357 / Symmetry type: POINT |