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Open data
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Basic information
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Title | Structure of lambda repressor in complex with RecA filament | |||||||||
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![]() | SOS response / RecA / lambda repressor / Filament / DNA repair / Helical reconstruction / DNA BINDING PROTEIN-DNA COMPLEX | |||||||||
Function / homology | ![]() maintenance of viral latency / DNA polymerase V complex / latency-replication decision / positive regulation of viral transcription / homologous recombination / negative regulation of transcription by competitive promoter binding / recombinational repair / ATP-dependent DNA damage sensor activity / response to ionizing radiation / SOS response ...maintenance of viral latency / DNA polymerase V complex / latency-replication decision / positive regulation of viral transcription / homologous recombination / negative regulation of transcription by competitive promoter binding / recombinational repair / ATP-dependent DNA damage sensor activity / response to ionizing radiation / SOS response / ATP-dependent activity, acting on DNA / translesion synthesis / core promoter sequence-specific DNA binding / cell motility / single-stranded DNA binding / DNA-binding transcription factor binding / DNA recombination / damaged DNA binding / DNA damage response / ATP hydrolysis activity / ATP binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 2.78 Å | |||||||||
![]() | Gao B / Feng Y | |||||||||
Funding support | ![]()
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![]() | ![]() 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
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 37.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.1 KB 16.1 KB | Display Display | ![]() |
Images | ![]() | 560.1 KB | ||
Filedesc metadata | ![]() | 5.8 KB | ||
Others | ![]() ![]() | 31.2 MB 31.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 887.6 KB | Display | ![]() |
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Full document | ![]() | 887.1 KB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Data in CIF | ![]() | 12.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8gmuMC ![]() 7ywaC ![]() 8gmsC ![]() 8gmtC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.19 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_34154_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34154_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : RecA-CI complex
Entire | Name: RecA-CI complex |
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Components |
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-Supramolecule #1: RecA-CI complex
Supramolecule | Name: RecA-CI complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Repressor protein cI
Macromolecule | Name: Repressor protein cI / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 14.999833 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: YEYPVFSHVQ AGMFSPELRT FTKGDAERWV STTKKASDSA FWLEVEGNSM TAPTGSKPSF PDGMLILVDP EQAVEPGDFC IARLGGDEF TFAKLIRDSG QVFLQPLNPQ YPMIPCNESC SVVGKVIASQ WPEETFG UniProtKB: Repressor protein cI |
-Macromolecule #2: Protein RecA
Macromolecule | Name: Protein RecA / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 38.016277 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MAIDENKQKA LAAALGQIEK QFGKGSIMRL GEDRSMDVET ISTGSLSLDI ALGAGGLPMG RIVEIYGPES SGKTTLTLQV IAAAQREGK TCAFIDAEHA LDPIYARKLG VDIDNLLCSQ PDTGEQALEI CDALARSGAV DVIVVDSVAA LTPKAEIEGE I GDSHMGLA ...String: MAIDENKQKA LAAALGQIEK QFGKGSIMRL GEDRSMDVET ISTGSLSLDI ALGAGGLPMG RIVEIYGPES SGKTTLTLQV IAAAQREGK TCAFIDAEHA LDPIYARKLG VDIDNLLCSQ PDTGEQALEI CDALARSGAV DVIVVDSVAA LTPKAEIEGE I GDSHMGLA ARMMSQAMRK LAGNLKQSNT LLIFINQIRM KIGVMFGNPE TTTGGNALKF YASVRLDIRR IGAVKEGENV VG SETRVKV VKNKIAAPFK QAEFQILYGE GINFYGELVD LGVKEKLIEK AGAWYSYKGE KIGQGKANAT AWLKDNPETA KEI EKKVRE LLLSNPNSTP DFSVDDSEGV AETNEDF UniProtKB: Protein RecA |
-Macromolecule #3: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
Macromolecule | Name: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3') / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 1.780199 KDa |
Sequence | String: (DT)(DT)(DT)(DT)(DT)(DT) |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 5 / Number of copies: 2 / Formula: AGS |
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Molecular weight | Theoretical: 523.247 Da |
Chemical component information | ![]() ChemComp-AGS: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | helical array |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 31.5 Å Applied symmetry - Helical parameters - Δ&Phi: 118.1 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 500031 |
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Startup model | Type of model: EMDB MAP EMDB ID: |
Final angle assignment | Type: NOT APPLICABLE |