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Yorodumi- EMDB-2808: Electron cryo-microscopy of the HerA-NurA double strand break res... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2808 | |||||||||
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Title | Electron cryo-microscopy of the HerA-NurA double strand break resection complex | |||||||||
Map data | Reconstruction of the HerA-NurA double strand break resection complex from Sulfolobus solfataricus | |||||||||
Sample |
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Keywords | Helicase / Nuclease / FtsK/HerA ATPase / DNA double-strand break repair / DNA resection | |||||||||
Function / homology | Function and homology information nuclease activity / helicase activity / DNA helicase / Hydrolases; Acting on ester bonds / DNA repair / ATP hydrolysis activity / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Sulfolobus solfataricus (archaea) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.35 Å | |||||||||
Authors | Byrne RT / Schuller JM / Unverdorben P / Foerster F / Hopfner K-P | |||||||||
Citation | Journal: FEBS Lett / Year: 2014 Title: Molecular architecture of the HerA-NurA DNA double-strand break resection complex. Authors: Robert Thomas Byrne / Jan Michael Schuller / Pia Unverdorben / Friedrich Förster / Karl-Peter Hopfner / Abstract: DNA double-strand breaks can be repaired by homologous recombination, during which the DNA ends are long-range resected by helicase-nuclease systems to generate 3' single strand tails. In archaea, ...DNA double-strand breaks can be repaired by homologous recombination, during which the DNA ends are long-range resected by helicase-nuclease systems to generate 3' single strand tails. In archaea, this requires the Mre11-Rad50 complex and the ATP-dependent helicase-nuclease complex HerA-NurA. We report the cryo-EM structure of Sulfolobus solfataricus HerA-NurA at 7.4Å resolution and present the pseudo-atomic model of the complex. HerA forms an ASCE hexamer that tightly interacts with a NurA dimer, with each NurA protomer binding three adjacent HerA HAS domains. Entry to NurA's nuclease active sites requires dsDNA to pass through a 23Å wide channel in the HerA hexamer. The structure suggests that HerA is a dsDNA translocase that feeds DNA into the NurA nuclease sites. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2808.map.gz | 2.1 MB | EMDB map data format | |
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Header (meta data) | emd-2808-v30.xml emd-2808.xml | 10.8 KB 10.8 KB | Display Display | EMDB header |
Images | EMD-2808.tif emd_2808.tif | 1 MB 1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2808 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2808 | HTTPS FTP |
-Validation report
Summary document | emd_2808_validation.pdf.gz | 226 KB | Display | EMDB validaton report |
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Full document | emd_2808_full_validation.pdf.gz | 225.1 KB | Display | |
Data in XML | emd_2808_validation.xml.gz | 5.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2808 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2808 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2808.map.gz / Format: CCP4 / Size: 12.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of the HerA-NurA double strand break resection complex from Sulfolobus solfataricus | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.77 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : HerA from Sulfolobus Solfataricus NurA from Sulfolobus Solfataricus
Entire | Name: HerA from Sulfolobus Solfataricus NurA from Sulfolobus Solfataricus |
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Components |
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-Supramolecule #1000: HerA from Sulfolobus Solfataricus NurA from Sulfolobus Solfataricus
Supramolecule | Name: HerA from Sulfolobus Solfataricus NurA from Sulfolobus Solfataricus type: sample / ID: 1000 / Details: The sample was monodisperse Oligomeric state: One homohexamer of HerA binds to one homodimer of NurA Number unique components: 2 |
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Molecular weight | Experimental: 419 KDa / Theoretical: 416 KDa / Method: SEC-RALS |
-Macromolecule #1: HerA
Macromolecule | Name: HerA / type: protein_or_peptide / ID: 1 / Name.synonym: SSO2251 / Number of copies: 6 / Oligomeric state: homohexamer / Recombinant expression: Yes |
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Source (natural) | Organism: Sulfolobus solfataricus (archaea) / Strain: P2 |
Molecular weight | Theoretical: 56 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: Rosetta / Recombinant plasmid: pET-Duet-1 |
Sequence | UniProtKB: DNA double-strand break repair helicase HerA |
-Macromolecule #2: NurA
Macromolecule | Name: NurA / type: protein_or_peptide / ID: 2 / Name.synonym: SSO2248 / Number of copies: 2 / Oligomeric state: dimer / Recombinant expression: Yes |
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Source (natural) | Organism: Sulfolobus solfataricus (archaea) / Strain: P2 |
Molecular weight | Theoretical: 39 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: Rosetta / Recombinant plasmid: pET-Duet-1 |
Sequence | UniProtKB: DNA double-strand break repair nuclease NurA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.05 mg/mL |
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Buffer | pH: 8 / Details: 100 mM NaCl, 20 mM Hepes |
Grid | Details: 2:1 holey carbon grids (Quantifoil Micro Tools, Germany) |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 93 K / Instrument: HOMEMADE PLUNGER Method: Blot for 2 seconds before plunging, wash twice with water |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification |
Specialist optics | Energy filter - Name: GIF QUANTUM / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Date | Aug 22, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 863 / Average electron dose: 25 e/Å2 Details: Every image is the average of 20 frames recorded by the direct electron detector |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | The particles were semi-manually selected in e2boxer and further processed in RELION |
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CTF correction | Details: On the micrograph level |
Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.35 Å / Resolution method: OTHER / Software - Name: RELION / Details: see detailed method in paper / Number images used: 100000 |