[English] 日本語
Yorodumi- PDB-7z03: Endonuclease state of the E. coli Mre11-Rad50 (SbcCD) head comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7z03 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Endonuclease state of the E. coli Mre11-Rad50 (SbcCD) head complex bound to ADP and extended dsDNA | |||||||||
Components |
| |||||||||
Keywords | DNA BINDING PROTEIN / ABC-type ATPase / Nuclease / DNA repair | |||||||||
Function / homology | Function and homology information double-stranded DNA endonuclease activity / DNA exonuclease activity / single-stranded DNA endodeoxyribonuclease activity / 3'-5'-DNA exonuclease activity / DNA repair complex / 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 / 3'-5'-DNA exonuclease activity / DNA repair complex / 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 | Escherichia coli (E. coli) synthetic construct (others) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Gut, F. / Kaeshammer, L. / Lammens, K. / Bartho, J. / van de Logt, E. / Kessler, B. / Hopfner, K.P. | |||||||||
Funding support | European Union, Germany, 2items
| |||||||||
Citation | Journal: Mol Cell / Year: 2022 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: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7z03.cif.gz | 374 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7z03.ent.gz | 274.2 KB | Display | PDB format |
PDBx/mmJSON format | 7z03.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z03_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7z03_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7z03_validation.xml.gz | 51.3 KB | Display | |
Data in CIF | 7z03_validation.cif.gz | 77.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z0/7z03 ftp://data.pdbj.org/pub/pdb/validation_reports/z0/7z03 | HTTPS FTP |
-Related structure data
Related structure data | 14403MC 7yzoC 7yzpC C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-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 Source: (gene. exp.) Escherichia coli (E. coli) / Gene: sbcC, rmuA, b0397, JW0387 / Production host: Escherichia coli (E. coli) / References: UniProt: P13458 #2: Protein | Mass: 45640.277 Da / Num. of mol.: 2 / Mutation: H84Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: sbcD, yajA, b0398, JW0388 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG76 |
---|
-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
#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: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
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
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
---|---|
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57747 / Symmetry type: POINT |