+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15804 | ||||||||||||
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Title | RecBCD-DNA in complex with the phage protein Abc2 | ||||||||||||
Map data | Final cryoEM map of the RecBCD-Abc2-DNA complex | ||||||||||||
Sample |
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Function / homology | Function and homology information exodeoxyribonuclease V / exodeoxyribonuclease V activity / exodeoxyribonuclease V complex / DNA 5'-3' helicase / clearance of foreign intracellular DNA / DNA 3'-5' helicase / recombinational repair / single-stranded DNA helicase activity / 3'-5' DNA helicase activity / DNA helicase activity ...exodeoxyribonuclease V / exodeoxyribonuclease V activity / exodeoxyribonuclease V complex / DNA 5'-3' helicase / clearance of foreign intracellular DNA / DNA 3'-5' helicase / recombinational repair / single-stranded DNA helicase activity / 3'-5' DNA helicase activity / DNA helicase activity / isomerase activity / helicase activity / double-strand break repair via homologous recombination / response to radiation / 5'-3' DNA helicase activity / DNA recombination / DNA damage response / magnesium ion binding / ATP hydrolysis activity / DNA binding / ATP binding / cytosol Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (E. coli) / synthetic construct (others) / Salmonella phage P22 (virus) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||||||||
Authors | Wilkinson M / Wilkinson OJ / Feyerherm C / Fletcher EE / Wigley DB / Dillingham MS | ||||||||||||
Funding support | United Kingdom, 3 items
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Citation | Journal: Elife / Year: 2022 Title: Structures of RecBCD in complex with phage-encoded inhibitor proteins reveal distinctive strategies for evasion of a bacterial immunity hub. Authors: Martin Wilkinson / Oliver J Wilkinson / Connie Feyerherm / Emma E Fletcher / Dale B Wigley / Mark S Dillingham / Abstract: Following infection of bacterial cells, bacteriophage modulate double-stranded DNA break repair pathways to protect themselves from host immunity systems and prioritise their own recombinases. Here, ...Following infection of bacterial cells, bacteriophage modulate double-stranded DNA break repair pathways to protect themselves from host immunity systems and prioritise their own recombinases. Here, we present biochemical and structural analysis of two phage proteins, gp5.9 and Abc2, which target the DNA break resection complex RecBCD. These exemplify two contrasting mechanisms for control of DNA break repair in which the RecBCD complex is either inhibited or co-opted for the benefit of the invading phage. Gp5.9 completely inhibits RecBCD by preventing it from binding to DNA. The RecBCD-gp5.9 structure shows that gp5.9 acts by substrate mimicry, binding predominantly to the RecB arm domain and competing sterically for the DNA binding site. Gp5.9 adopts a parallel coiled-coil architecture that is unprecedented for a natural DNA mimic protein. In contrast, binding of Abc2 does not substantially affect the biochemical activities of isolated RecBCD. The RecBCD-Abc2 structure shows that Abc2 binds to the Chi-recognition domains of the RecC subunit in a position that might enable it to mediate the loading of phage recombinases onto its single-stranded DNA products. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15804.map.gz | 43.8 MB | EMDB map data format | |
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Header (meta data) | emd-15804-v30.xml emd-15804.xml | 28.3 KB 28.3 KB | Display Display | EMDB header |
Images | emd_15804.png | 99.9 KB | ||
Others | emd_15804_half_map_1.map.gz emd_15804_half_map_2.map.gz | 36.8 MB 36.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15804 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15804 | HTTPS FTP |
-Validation report
Summary document | emd_15804_validation.pdf.gz | 813.5 KB | Display | EMDB validaton report |
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Full document | emd_15804_full_validation.pdf.gz | 813 KB | Display | |
Data in XML | emd_15804_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | emd_15804_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15804 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15804 | HTTPS FTP |
-Related structure data
Related structure data | 8b1tMC 8b1rC 8b1uC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_15804.map.gz / Format: CCP4 / Size: 47.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Final cryoEM map of the RecBCD-Abc2-DNA complex | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: halfmap1
File | emd_15804_half_map_1.map | ||||||||||||
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Annotation | halfmap1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: halfmap2
File | emd_15804_half_map_2.map | ||||||||||||
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Annotation | halfmap2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : RecBCD-Abc2-DNA complex
+Supramolecule #1: RecBCD-Abc2-DNA complex
+Supramolecule #2: RecBCD enzyme subunit RecB, RecC and RecD
+Supramolecule #3: DNA (70-MER)
+Supramolecule #4: Anti-RecBCD protein 2
+Macromolecule #1: RecBCD enzyme subunit RecB
+Macromolecule #2: RecBCD enzyme subunit RecC
+Macromolecule #3: RecBCD enzyme subunit RecD
+Macromolecule #5: Anti-RecBCD protein 2
+Macromolecule #4: DNA (70-MER)
+Macromolecule #6: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
+Macromolecule #7: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: C-flat-2/1 / Material: COPPER / Mesh: 400 / Support film - Material: GRAPHENE OXIDE Details: Mixture of graphene oxide with 0.3 mM DDM detergent applied directly to grids twice before application of sample | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK IV / Details: 1.5s blot time. | ||||||||||||||||||
Details | RecBCD-Abc2 mixed with 1.5x molar excess of synthesised DNA substrate, 2 mM ADPNP and 5 mM MgCl2 prior to making grids |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2500 / Average exposure time: 12.0 sec. / Average electron dose: 56.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |