+Open data
-Basic information
Entry | Database: PDB / ID: 8a93 | ||||||
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Title | Complex of RecF-RecR-DNA from Thermus thermophilus. | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / DNA Repair pathway / RecFOR pathway / Thermus thermophilus | ||||||
Function / homology | Function and homology information SOS response / single-stranded DNA binding / DNA recombination / DNA replication / DNA repair / DNA binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus HB8 (bacteria) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.05 Å | ||||||
Authors | Nirwal, S. / Czarnocki-Cieciura, M. / Chaudhary, A. / Zajko, W. / Skowronek, K. / Chamera, S. / Figiel, M. / Nowotny, M. | ||||||
Funding support | Poland, 1items
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Citation | Journal: Nat Struct Mol Biol / Year: 2023 Title: Mechanism of RecF-RecO-RecR cooperation in bacterial homologous recombination. Authors: Shivlee Nirwal / Mariusz Czarnocki-Cieciura / Anuradha Chaudhary / Weronika Zajko / Krzysztof Skowronek / Sebastian Chamera / Małgorzata Figiel / Marcin Nowotny / Abstract: In bacteria, one type of homologous-recombination-based DNA-repair pathway involves RecFOR proteins that bind at the junction between single-stranded (ss) and double-stranded (ds) DNA. They ...In bacteria, one type of homologous-recombination-based DNA-repair pathway involves RecFOR proteins that bind at the junction between single-stranded (ss) and double-stranded (ds) DNA. They facilitate the replacement of SSB protein, which initially covers ssDNA, with RecA, which mediates the search for homologous sequences. However, the molecular mechanism of RecFOR cooperation remains largely unknown. We used Thermus thermophilus proteins to study this system. Here, we present a cryo-electron microscopy structure of the RecF-dsDNA complex, and another reconstruction that shows how RecF interacts with two different regions of the tetrameric RecR ring. Lower-resolution reconstructions of the RecR-RecO subcomplex and the RecFOR-DNA assembly explain how RecO is positioned to interact with ssDNA and SSB, which is proposed to lock the complex on a ssDNA-dsDNA junction. Our results integrate the biochemical data available for the RecFOR system and provide a framework for its complete understanding. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a93.cif.gz | 186.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a93.ent.gz | 136.2 KB | Display | PDB format |
PDBx/mmJSON format | 8a93.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8a93_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8a93_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8a93_validation.xml.gz | 44.3 KB | Display | |
Data in CIF | 8a93_validation.cif.gz | 63.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/8a93 ftp://data.pdbj.org/pub/pdb/validation_reports/a9/8a93 | HTTPS FTP |
-Related structure data
Related structure data | 15267MC 8a8jC 8ab0C 8bprC 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
-Protein , 2 types, 5 molecules ABCDF
#1: Protein | Mass: 37933.715 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: ATCC 27634 / DSM 579 / HB8 / Gene: recF / Production host: Escherichia coli (E. coli) / Strain (production host): Arctic Express / References: UniProt: Q5SLM9 #2: Protein | Mass: 21323.467 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: ATCC 27634 / DSM 579 / HB8 / Gene: recR, TTHA1600 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star / References: UniProt: Q5SHY0 |
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-DNA chain , 2 types, 2 molecules XY
#3: DNA chain | Mass: 7661.912 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#4: DNA chain | Mass: 12395.925 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 2 types, 4 molecules
#5: Chemical | #6: Chemical | |
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-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 | Name: Complex of RecF-RecR-DNA from Thermus thermophilus. / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.18 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Thermus thermophilus HB8 (bacteria) | ||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Sample fixed with 0.05% glutaraldehyde and concentrated prior to vitrification; exact concentration cannot be estimated accurately. | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: C-flat-2/1 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K |
-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: 105000 X / Nominal defocus max: 2700 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 41.71 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7217 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2381100 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 318235 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 106.32 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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