[English] 日本語
![](img/lk-miru.gif)
- PDB-7yzo: Endonuclease state of the E. coli Mre11-Rad50 (SbcCD) head comple... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7yzo | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Endonuclease state of the E. coli Mre11-Rad50 (SbcCD) head complex bound to ADP and dsDNA | |||||||||
![]() |
| |||||||||
![]() | DNA BINDING PROTEIN / ABC-type ATPase / Nuclease / DNA repair | |||||||||
Function / homology | ![]() double-stranded DNA endonuclease activity / DNA exonuclease activity / single-stranded DNA endodeoxyribonuclease activity / DNA repair complex / 3'-5'-DNA exonuclease activity / 3'-5' exonuclease activity / double-strand break repair / DNA recombination / DNA replication / DNA repair ...double-stranded DNA endonuclease activity / DNA exonuclease activity / single-stranded DNA endodeoxyribonuclease activity / DNA repair complex / 3'-5'-DNA exonuclease activity / 3'-5' exonuclease activity / double-strand break repair / DNA recombination / DNA replication / DNA repair / ATP hydrolysis activity / DNA binding / ATP binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() synthetic construct (others) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Gut, F. / Kaeshammer, L. / Lammens, K. / Bartho, J. / van de Logt, E. / Kessler, B. / Hopfner, K.P. | |||||||||
Funding support | European Union, ![]()
| |||||||||
![]() | ![]() Title: Structural mechanism of endonucleolytic processing of blocked DNA ends and hairpins by Mre11-Rad50. Authors: Fabian Gut / Lisa Käshammer / Katja Lammens / Joseph D Bartho / Anna-Maria Boggusch / Erik van de Logt / Brigitte Kessler / Karl-Peter Hopfner / ![]() Abstract: DNA double-strand breaks (DSBs) threaten genome stability and are linked to tumorigenesis in humans. Repair of DSBs requires the removal of attached proteins and hairpins through a poorly understood ...DNA double-strand breaks (DSBs) threaten genome stability and are linked to tumorigenesis in humans. Repair of DSBs requires the removal of attached proteins and hairpins through a poorly understood but physiologically critical endonuclease activity by the Mre11-Rad50 complex. Here, we report cryoelectron microscopy (cryo-EM) structures of the bacterial Mre11-Rad50 homolog SbcCD bound to a protein-blocked DNA end and a DNA hairpin. The structures reveal that Mre11-Rad50 bends internal DNA for endonucleolytic cleavage and show how internal DNA, DNA ends, and hairpins are processed through a similar ATP-regulated conformational state. Furthermore, Mre11-Rad50 is loaded onto blocked DNA ends with Mre11 pointing away from the block, explaining the distinct biochemistries of 3' → 5' exonucleolytic and endonucleolytic incision through the way Mre11-Rad50 interacts with diverse DNA ends. In summary, our results unify Mre11-Rad50's enigmatic nuclease diversity within a single structural framework and reveal how blocked DNA ends and hairpins are processed. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 367.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 268.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 14391MC ![]() 7yzpC ![]() 7z03C 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
-Nuclease SbcCD subunit ... , 2 types, 4 molecules CDAB
#1: Protein | Mass: 118851.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: A large part of the structure in the middle of the sequence is missing. Therefore the alignment is not correct. The C-terminal part misaligns to the middle domain of the sequence. Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 45640.277 Da / Num. of mol.: 2 / Mutation: H84Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-DNA chain , 2 types, 2 molecules EF
#3: DNA chain | Mass: 37099.617 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: GenBank: 1825215262 |
---|---|
#4: DNA chain | Mass: 36970.527 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: GenBank: 1825215262 |
-Non-polymers , 3 types, 8 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MN.gif)
#5: Chemical | #6: Chemical | #7: Chemical | ChemComp-MN / |
---|
-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: Complex of Mre11 dimer, Rad50 dimer and double-stranded DNA Type: COMPLEX / Entity ID: #1-#4 / 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: 2800 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 43.19 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-
Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 199751 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|