+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21996 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Mfd-bound E.coli RNA polymerase elongation complex - L1 state | |||||||||
Map data | Cryo-EM map, sharpened | |||||||||
Sample |
| |||||||||
Keywords | Transcription-coupled DNA repair / DNA translocase / elongation complex / RNA polymerase / TRANSCRIPTION / TRANSCRIPTION-RNA-DNA complex | |||||||||
Function / homology | Function and homology information transcription-coupled nucleotide-excision repair, DNA damage recognition / RNA polymerase core enzyme binding / DNA translocase activity / nucleotide-excision repair, preincision complex assembly / DNA repair complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation ...transcription-coupled nucleotide-excision repair, DNA damage recognition / RNA polymerase core enzyme binding / DNA translocase activity / nucleotide-excision repair, preincision complex assembly / DNA repair complex / RNA polymerase complex / 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 / transcription-coupled nucleotide-excision repair / nitrate assimilation / DNA-directed RNA polymerase complex / DNA helicase activity / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription initiation / cell motility / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / damaged DNA binding / protein dimerization activity / hydrolase activity / DNA repair / response to antibiotic / DNA-templated transcription / DNA damage response / regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / ATP binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
Authors | Llewellyn E / Chen J | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: Elife / Year: 2021 Title: Structural basis for transcription complex disruption by the Mfd translocase. Authors: Jin Young Kang / Eliza Llewellyn / James Chen / Paul Dominic B Olinares / Joshua Brewer / Brian T Chait / Elizabeth A Campbell / Seth A Darst / Abstract: Transcription-coupled repair (TCR) is a sub-pathway of nucleotide excision repair (NER) that preferentially removes lesions from the template-strand (t-strand) that stall RNA polymerase (RNAP) ...Transcription-coupled repair (TCR) is a sub-pathway of nucleotide excision repair (NER) that preferentially removes lesions from the template-strand (t-strand) that stall RNA polymerase (RNAP) elongation complexes (ECs). Mfd mediates TCR in bacteria by removing the stalled RNAP concealing the lesion and recruiting Uvr(A)BC. We used cryo-electron microscopy to visualize Mfd engaging with a stalled EC and attempting to dislodge the RNAP. We visualized seven distinct Mfd-EC complexes in both ATP and ADP-bound states. The structures explain how Mfd is remodeled from its repressed conformation, how the UvrA-interacting surface of Mfd is hidden during most of the remodeling process to prevent premature engagement with the NER pathway, how Mfd alters the RNAP conformation to facilitate disassembly, and how Mfd forms a processive translocation complex after dislodging the RNAP. Our results reveal an elaborate mechanism for how Mfd kinetically discriminates paused from stalled ECs and disassembles stalled ECs to initiate TCR. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21996.map.gz | 96.5 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-21996-v30.xml emd-21996.xml | 26.9 KB 26.9 KB | Display Display | EMDB header |
Images | emd_21996.png | 54.4 KB | ||
Filedesc metadata | emd-21996.cif.gz | 9.5 KB | ||
Others | emd_21996_additional_1.map.gz | 4.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21996 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21996 | HTTPS FTP |
-Validation report
Summary document | emd_21996_validation.pdf.gz | 619.2 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_21996_full_validation.pdf.gz | 618.7 KB | Display | |
Data in XML | emd_21996_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | emd_21996_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21996 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21996 | HTTPS FTP |
-Related structure data
Related structure data | 6x26MC 6x2fC 6x2nC 6x43C 6x4wC 6x4yC 6x50C C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_21996.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Cryo-EM map, sharpened | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Additional map: Cryo-EM map, local resolution filtered
File | emd_21996_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Cryo-EM map, local resolution filtered | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : Escherichia coli Mfd-RNAP elonation complex: state L1
+Supramolecule #1: Escherichia coli Mfd-RNAP elonation complex: state L1
+Macromolecule #1: Transcription-repair-coupling factor
+Macromolecule #2: DNA-directed RNA polymerase subunit alpha
+Macromolecule #3: DNA-directed RNA polymerase subunit beta
+Macromolecule #4: DNA-directed RNA polymerase subunit beta'
+Macromolecule #5: DNA-directed RNA polymerase subunit omega
+Macromolecule #6: RNA (20-MER)
+Macromolecule #7: DNA (64-MER)
+Macromolecule #8: DNA (64-MER)
+Macromolecule #9: MAGNESIUM ION
+Macromolecule #10: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 / Component - Concentration: 20.0 mM / Component - Name: Tris-HCl |
---|---|
Grid | Model: C-flat-1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 22 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |