+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34153 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of UmuD in complex with RecA filament | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | SOS response / RecA / UmuD / Filament / DNA repair / Helical Reconstruction / DNA BINDING PROTEIN-DNA COMPLEX | |||||||||
Function / homology | Function and homology information repressor LexA / SOS response / ATP-dependent DNA damage sensor activity / 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 / SOS response / ATP-dependent DNA damage sensor activity / 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 | helical reconstruction / cryo EM / Resolution: 3.31 Å | |||||||||
Authors | Gao B / Feng Y | |||||||||
Funding support | China, 1 items
| |||||||||
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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_34153.map.gz | 37.9 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-34153-v30.xml emd-34153.xml | 16.2 KB 16.2 KB | Display Display | EMDB header |
Images | emd_34153.png | 537.2 KB | ||
Masks | emd_34153_msk_1.map | 40.6 MB | Mask map | |
Filedesc metadata | emd-34153.cif.gz | 5.8 KB | ||
Others | emd_34153_half_map_1.map.gz emd_34153_half_map_2.map.gz | 31.3 MB 31.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34153 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34153 | HTTPS FTP |
-Validation report
Summary document | emd_34153_validation.pdf.gz | 957.1 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_34153_full_validation.pdf.gz | 956.7 KB | Display | |
Data in XML | emd_34153_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | emd_34153_validation.cif.gz | 13 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34153 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34153 | HTTPS FTP |
-Related structure data
Related structure data | 8gmtMC 7ywaC 8gmsC 8gmuC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_34153.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.19 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | emd_34153_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_34153_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_34153_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : RecA-UmuD complex
Entire | Name: RecA-UmuD complex |
---|---|
Components |
|
-Supramolecule #1: RecA-UmuD complex
Supramolecule | Name: RecA-UmuD complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
---|---|
Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: DNA polymerase V subunit UmuD
Macromolecule | Name: DNA polymerase V subunit UmuD / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: repressor LexA |
---|---|
Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 15.017207 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MLFIKPADLR EIVTFPLFSD LVQCGFPSPA ADYVEQRIDL NQLLIQHPSA TYFVKASGDS MIDGGISDGD LLIVDSAITA SHGDIVIAA VDGEFTVAKL QLRPTVQLIP MNSAYSPITI SSEDTLDVFG VVIHVVKAMR UniProtKB: DNA polymerase V subunit UmuD |
-Macromolecule #3: Protein RecA
Macromolecule | Name: Protein RecA / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 38.016277 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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 #2: 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: 2 / Number of copies: 1 / Classification: DNA |
---|---|
Source (natural) | Organism: Escherichia coli (E. coli) |
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 |
---|---|
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 |
---|---|
Molecular weight | Theoretical: 523.247 Da |
Chemical component information | ChemComp-AGS: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 52.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
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 |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 31.6 Å Applied symmetry - Helical parameters - Δ&Phi: 118.3 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 137040 |
---|---|
Startup model | Type of model: EMDB MAP EMDB ID: |
Final angle assignment | Type: NOT APPLICABLE |