+Open data
-Basic information
Entry | Database: PDB / ID: 8b1t | ||||||||||||
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Title | RecBCD-DNA in complex with the phage protein Abc2 | ||||||||||||
Components |
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Keywords | DNA BINDING PROTEIN / Homologous recombination / DNA repair / phage / Helicase / Nuclease / Inhibitor / Protein complex / Enzyme / DNA mimic | ||||||||||||
Function / homology | Function and homology information exodeoxyribonuclease V / exodeoxyribonuclease V activity / exodeoxyribonuclease V complex / clearance of foreign intracellular DNA / DNA 5'-3' helicase / single-stranded DNA helicase activity / DNA 3'-5' helicase / recombinational repair / 3'-5' DNA helicase activity / DNA helicase activity ...exodeoxyribonuclease V / exodeoxyribonuclease V activity / exodeoxyribonuclease V complex / clearance of foreign intracellular DNA / DNA 5'-3' helicase / single-stranded DNA helicase activity / DNA 3'-5' helicase / recombinational repair / 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 Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (E. coli) Salmonella phage P22 (virus) synthetic construct (others) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||||||||
Authors | Wilkinson, M. / Wilkinson, O.J. / Feyerherm, C. / Fletcher, E.E. / Wigley, D.B. / Dillingham, M.S. | ||||||||||||
Funding support | United Kingdom, 3items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b1t.cif.gz | 543.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b1t.ent.gz | 431 KB | Display | PDB format |
PDBx/mmJSON format | 8b1t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8b1t_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8b1t_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8b1t_validation.xml.gz | 79.8 KB | Display | |
Data in CIF | 8b1t_validation.cif.gz | 120.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/8b1t ftp://data.pdbj.org/pub/pdb/validation_reports/b1/8b1t | HTTPS FTP |
-Related structure data
Related structure data | 15804MC 8b1rC 8b1uC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RecBCD enzyme subunit ... , 3 types, 3 molecules BCD
#1: Protein | Mass: 134066.625 Da / Num. of mol.: 1 / Mutation: D1080A Source method: isolated from a genetically manipulated source Details: Nuclease-dead mutant D1080A / Source: (gene. exp.) Escherichia coli (E. coli) Gene: recB, BHS81_16925, BJI68_00835, BON89_01565, BON93_20715, BvCmsHHP056_02020, C5N07_06355, C5Y87_19730, C9114_10810, DAH36_05180, DAH37_01130, E2134_07940, E5M02_13555, E5P30_22870, E5P31_10440, ...Gene: recB, BHS81_16925, BJI68_00835, BON89_01565, BON93_20715, BvCmsHHP056_02020, C5N07_06355, C5Y87_19730, C9114_10810, DAH36_05180, DAH37_01130, E2134_07940, E5M02_13555, E5P30_22870, E5P31_10440, E5P32_13260, E5P36_03520, E5P40_11525, E5P51_08340, E5S39_06465, E5S44_07560, EI021_14360, ELX85_18530, EYV17_10125, EYV18_15060, F0L67_06605, F2N31_08115, F9V24_07045, FOI11_01100, FOI11_022080, GF699_18635, GKF89_09600, GRW05_08565, HMV95_04145, HX136_04845, IH772_15520, JNP96_21695, NCTC13216_00866, NCTC9117_01550, NCTC9706_03254, RG28_07470 Plasmid: pRSFduet / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A024LB08, exodeoxyribonuclease V |
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#2: Protein | Mass: 128974.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: recC, b2822, JW2790 / Plasmid: pRSFduet / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P07648, exodeoxyribonuclease V |
#3: Protein | Mass: 66990.367 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: recD, hopE, b2819, JW2787 / Plasmid: pCDFduet / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P04993, exodeoxyribonuclease V |
-DNA chain / Protein , 2 types, 2 molecules XA
#4: DNA chain | Mass: 21440.707 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Synthesised hairpin substrate with unpaired ssDNA tails Source: (synth.) synthetic construct (others) |
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#5: Protein | Mass: 11640.210 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella phage P22 (virus) / Gene: abc2 / Plasmid: pET22b / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P11191 |
-Non-polymers , 2 types, 2 molecules
#6: Chemical | ChemComp-ANP / |
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#7: Chemical | ChemComp-MG / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | |||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: RecBCD-Abc2 mixed with 1.5x molar excess of synthesised DNA substrate, 2 mM ADPNP and 5 mM MgCl2 prior to making grids | |||||||||||||||||||||||||||||||||||
Specimen support | Details: Mixture of graphene oxide with 0.3 mM DDM detergent applied directly to grids twice before application of sample Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-2/1 | |||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Details: 1.5s blot time |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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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 magnification: 130000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 12 sec. / Electron dose: 56 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2500 |
EM imaging optics | Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 467613 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119163 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 72 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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