[English] 日本語
Yorodumi- EMDB-30117: CryoEM structure of Thermus thermophilus transcription-repair cou... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30117 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CryoEM structure of Thermus thermophilus transcription-repair coupling complex in the absence of ATP-gamma-S | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | Transcription / RNA polymerase / DNA repair / Mfd | |||||||||
Function / homology | Function and homology information transcription-coupled nucleotide-excision repair, DNA damage recognition / DNA-directed RNA polymerase complex / DNA helicase activity / 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 / damaged DNA binding / protein dimerization activity / hydrolase activity ...transcription-coupled nucleotide-excision repair, DNA damage recognition / DNA-directed RNA polymerase complex / DNA helicase activity / 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 / damaged DNA binding / protein dimerization activity / hydrolase activity / DNA-templated transcription / regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Thermus thermophilus (bacteria) / Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) / Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.0 Å | |||||||||
Authors | Shi J / Wen A | |||||||||
Funding support | China, 1 items
| |||||||||
Citation | Journal: Nucleic Acids Res / Year: 2020 Title: Structural basis of Mfd-dependent transcription termination. Authors: Jing Shi / Aijia Wen / Minxing Zhao / Sha Jin / Linlin You / Yue Shi / Shuling Dong / Xiaoting Hua / Yu Zhang / Yu Feng / Abstract: Mfd-dependent transcription termination plays an important role in transcription-coupled DNA repair, transcription-replication conflict resolution, and antimicrobial resistance development. Despite ...Mfd-dependent transcription termination plays an important role in transcription-coupled DNA repair, transcription-replication conflict resolution, and antimicrobial resistance development. Despite extensive studies, the molecular mechanism of Mfd-dependent transcription termination in bacteria remains unclear, with several long-standing puzzles. How Mfd is activated by stalled RNA polymerase (RNAP) and how activated Mfd translocates along the DNA are unknown. Here, we report the single-particle cryo-electron microscopy structures of T. thermophilus Mfd-RNAP complex with and without ATPγS. The structures reveal that Mfd undergoes profound conformational changes upon activation, contacts the RNAP β1 domain and its clamp, and pries open the RNAP clamp. These structures provide a foundation for future studies aimed at dissecting the precise mechanism of Mfd-dependent transcription termination and pave the way for rational drug design targeting Mfd for the purpose of tackling the antimicrobial resistance crisis. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30117.map.gz | 2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-30117-v30.xml emd-30117.xml | 19.8 KB 19.8 KB | Display Display | EMDB header |
Images | emd_30117.png | 54 KB | ||
Filedesc metadata | emd-30117.cif.gz | 8.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30117 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30117 | HTTPS FTP |
-Related structure data
Related structure data | 6m6aMC 6m6bC 6m6cC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_30117.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.307 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
+Entire : Thermus thermophilus transcription-coupled DNA repair complex
+Supramolecule #1: Thermus thermophilus transcription-coupled DNA repair complex
+Macromolecule #1: DNA-directed RNA polymerase subunit alpha
+Macromolecule #2: DNA-directed RNA polymerase subunit beta
+Macromolecule #3: DNA-directed RNA polymerase subunit beta'
+Macromolecule #4: DNA-directed RNA polymerase subunit omega
+Macromolecule #5: Transcription-repair-coupling factor
+Macromolecule #6: template strand DNA
+Macromolecule #7: nontemplate strand DNA
+Macromolecule #8: ZINC ION
+Macromolecule #9: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.9 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 59.0 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 |
-Image processing
Startup model | Type of model: PDB ENTRY |
---|---|
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 24037 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |