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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21996 | |||||||||
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Title | Mfd-bound E.coli RNA polymerase elongation complex - L1 state | |||||||||
![]() | Cryo-EM map, sharpened | |||||||||
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![]() | Transcription-coupled DNA repair / DNA translocase / elongation complex / ![]() ![]() | |||||||||
Function / homology | ![]() transcription-coupled nucleotide-excision repair, DNA damage recognition / RNA polymerase core enzyme binding / nucleotide-excision repair, preincision complex assembly / DNA translocase activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Llewellyn E / Chen J | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 96.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 26.9 KB 26.9 KB | Display Display | ![]() |
Images | ![]() | 54.4 KB | ||
Filedesc metadata | ![]() | 9.5 KB | ||
Others | ![]() | 4.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6x26MC ![]() 6x2fC ![]() 6x2nC ![]() 6x43C ![]() 6x4wC ![]() 6x4yC ![]() 6x50C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map, sharpened | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Cryo-EM map, local resolution filtered
File | emd_21996_additional_1.map | ||||||||||||
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Annotation | Cryo-EM map, local resolution filtered | ||||||||||||
Projections & Slices |
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Density Histograms |
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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 | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 / Component - Concentration: 20.0 mM / Component - Name: Tris-HCl![]() |
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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 |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: OTHER / Software - Name: cryoSPARC |
Final 3D classification | Software - Name: RELION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 13000 |