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Yorodumi- EMDB-26832: CryoEM Structure of E. coli Transcription-Coupled Ribonucleotide ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26832 | |||||||||
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Title | CryoEM Structure of E. coli Transcription-Coupled Ribonucleotide Excision Repair (TC-RER) complex bound to ribonucleotide substrate | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Transcription-coupled RER / TRANSCRIPTION / TRANSFERASE-HYDROLASE-DNA-RNA complex | |||||||||
Function / homology | Function and homology information ribonuclease H2 complex / DNA replication, removal of RNA primer / ribonuclease H / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / mismatch repair ...ribonuclease H2 complex / DNA replication, removal of RNA primer / ribonuclease H / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / mismatch repair / nitrate assimilation / DNA-directed RNA polymerase complex / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription initiation / cell motility / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / RNA-DNA hybrid ribonuclease activity / manganese ion binding / response to heat / intracellular iron ion homeostasis / protein dimerization activity / response to antibiotic / DNA-templated transcription / magnesium ion binding / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Hao ZT / Grower M / Bharati B / Proshkin S / Epshtein V / Svetlov V / Nudler E / Shamovsky I | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Cell / Year: 2023 Title: RNA polymerase drives ribonucleotide excision DNA repair in E. coli. Authors: Zhitai Hao / Manjunath Gowder / Sergey Proshkin / Binod K Bharati / Vitaly Epshtein / Vladimir Svetlov / Ilya Shamovsky / Evgeny Nudler / Abstract: Ribonuclease HII (RNaseHII) is the principal enzyme that removes misincorporated ribonucleoside monophosphates (rNMPs) from genomic DNA. Here, we present structural, biochemical, and genetic evidence ...Ribonuclease HII (RNaseHII) is the principal enzyme that removes misincorporated ribonucleoside monophosphates (rNMPs) from genomic DNA. Here, we present structural, biochemical, and genetic evidence demonstrating that ribonucleotide excision repair (RER) is directly coupled to transcription. Affinity pull-downs and mass-spectrometry-assisted mapping of in cellulo inter-protein cross-linking reveal the majority of RNaseHII molecules interacting with RNA polymerase (RNAP) in E. coli. Cryoelectron microscopy structures of RNaseHII bound to RNAP during elongation, with and without the target rNMP substrate, show specific protein-protein interactions that define the transcription-coupled RER (TC-RER) complex in engaged and unengaged states. The weakening of RNAP-RNaseHII interactions compromises RER in vivo. The structure-functional data support a model where RNaseHII scans DNA in one dimension in search for rNMPs while "riding" the RNAP. We further demonstrate that TC-RER accounts for a significant fraction of repair events, thereby establishing RNAP as a surveillance "vehicle" for detecting the most frequently occurring replication errors. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26832.map.gz | 61.8 MB | EMDB map data format | |
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Header (meta data) | emd-26832-v30.xml emd-26832.xml | 25 KB 25 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26832_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_26832.png | 91.4 KB | ||
Masks | emd_26832_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-26832.cif.gz | 8.5 KB | ||
Others | emd_26832_half_map_1.map.gz emd_26832_half_map_2.map.gz | 80.9 MB 80.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26832 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26832 | HTTPS FTP |
-Validation report
Summary document | emd_26832_validation.pdf.gz | 832.7 KB | Display | EMDB validaton report |
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Full document | emd_26832_full_validation.pdf.gz | 832.3 KB | Display | |
Data in XML | emd_26832_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | emd_26832_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26832 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26832 | HTTPS FTP |
-Related structure data
Related structure data | 7uwhMC 7uweC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26832.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.096 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_26832_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_26832_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_26832_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Elongation Complex(EC)-RNaseH2 complex bound to ribonucleotide su...
+Supramolecule #1: Elongation Complex(EC)-RNaseH2 complex bound to ribonucleotide su...
+Macromolecule #1: DNA (59-MER)
+Macromolecule #2: DNA/RNA (59-MER)
+Macromolecule #3: Ribonuclease HII
+Macromolecule #4: DNA-directed RNA polymerase subunit alpha
+Macromolecule #5: DNA-directed RNA polymerase subunit beta
+Macromolecule #6: DNA-directed RNA polymerase subunit beta'
+Macromolecule #7: DNA-directed RNA polymerase subunit omega
+Macromolecule #8: RNA (18-MER)
+Macromolecule #9: ZINC ION
+Macromolecule #10: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: OTHER |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 56.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |