+Open data
-Basic information
Entry | Database: PDB / ID: 8gmt | ||||||
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Title | Structure of UmuD in complex with RecA filament | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / SOS response / RecA / UmuD / Filament / DNA repair / Helical Reconstruction / DNA BINDING PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information repressor LexA / ATP-dependent DNA damage sensor activity / SOS response / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / single-stranded DNA binding / DNA recombination / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / hydrolase activity ...repressor LexA / ATP-dependent DNA damage sensor activity / SOS response / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / single-stranded DNA binding / DNA recombination / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / hydrolase activity / DNA repair / regulation of DNA-templated transcription / ATP hydrolysis activity / DNA binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.31 Å | ||||||
Authors | Gao, B. / Feng, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2023 Title: Structural basis for regulation of SOS response in bacteria. Authors: Bo Gao / Liang Liang / Lu Su / Aijia Wen / Chun Zhou / Yu Feng / Abstract: In response to DNA damage, bacterial RecA protein forms filaments with the assistance of DinI protein. The RecA filaments stimulate the autocleavage of LexA, the repressor of more than 50 SOS genes, ...In response to DNA damage, bacterial RecA protein forms filaments with the assistance of DinI protein. The RecA filaments stimulate the autocleavage of LexA, the repressor of more than 50 SOS genes, and activate the SOS response. During the late phase of SOS response, the RecA filaments stimulate the autocleavage of UmuD and λ repressor CI, leading to mutagenic repair and lytic cycle, respectively. Here, we determined the cryo-electron microscopy structures of RecA filaments in complex with DinI, LexA, UmuD, and λCI by helical reconstruction. The structures reveal that LexA and UmuD dimers bind in the filament groove and cleave in an intramolecular and an intermolecular manner, respectively, while λCI binds deeply in the filament groove as a monomer. Despite their distinct folds and oligomeric states, all RecA filament binders recognize the same conserved protein features in the filament groove. The SOS response in bacteria can lead to mutagenesis and antimicrobial resistance, and our study paves the way for rational drug design targeting the bacterial SOS response. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gmt.cif.gz | 159.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gmt.ent.gz | 126.4 KB | Display | PDB format |
PDBx/mmJSON format | 8gmt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/8gmt ftp://data.pdbj.org/pub/pdb/validation_reports/gm/8gmt | HTTPS FTP |
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-Related structure data
Related structure data | 34153MC 7ywaC 8gmsC 8gmuC M: map data used to model this data C: citing same article (ref.) |
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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
#1: Protein | Mass: 15017.207 Da / Num. of mol.: 2 / Mutation: K97A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: umuD / Production host: Escherichia coli (E. coli) References: UniProt: C3TD82, repressor LexA, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases, DNA-directed DNA polymerase #2: DNA chain | | Mass: 1780.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) #3: Protein | Mass: 38016.277 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: recA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A485JBB4 #4: Chemical | #5: Chemical | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: RecA-UmuD complex / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
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 |
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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 FIELDBright-field microscopy / Nominal defocus max: 1700 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 52 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Helical symmerty | Angular rotation/subunit: 118.3 ° / Axial rise/subunit: 31.6 Å / Axial symmetry: C1 |
3D reconstruction | Resolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 137040 / Symmetry type: HELICAL |