+Open data
-Basic information
Entry | Database: PDB / ID: 6x43 | ||||||
---|---|---|---|---|---|---|---|
Title | Mfd-bound E.coli RNA polymerase elongation complex - II state | ||||||
Components |
| ||||||
Keywords | TRANSCRIPTION / Transcription-coupled DNA repair / DNA translocase / elongation complex / RNA polymerase | ||||||
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 / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex ...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 / bacterial-type RNA polymerase core enzyme binding / 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 / DNA-templated transcription initiation / transcription antitermination / 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 / response to antibiotic / DNA repair / DNA-templated transcription / DNA damage response / regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / ATP binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||
Authors | Llewellyn, E. / Chen, J. / Kang, J.Y. / Darst, S.A. | ||||||
Funding support | United States, 1items
| ||||||
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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6x43.cif.gz | 815.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6x43.ent.gz | 648.5 KB | Display | PDB format |
PDBx/mmJSON format | 6x43.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6x43_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6x43_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6x43_validation.xml.gz | 113.6 KB | Display | |
Data in CIF | 6x43_validation.cif.gz | 177.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x4/6x43 ftp://data.pdbj.org/pub/pdb/validation_reports/x4/6x43 | HTTPS FTP |
-Related structure data
Related structure data | 22039MC 6x26C 6x2fC 6x2nC 6x4wC 6x4yC 6x50C M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules GHIJK
#2: Protein | Mass: 36558.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoA / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A073G207, UniProt: P0A7Z4*PLUS, DNA-directed RNA polymerase #3: Protein | | Mass: 150820.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoB, Z5560, ECs4910 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0A8V4, UniProt: P0A8V2*PLUS, DNA-directed RNA polymerase #4: Protein | | Mass: 155366.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoC, BvCmsKKP036_03580 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A4S1NBU2, UniProt: P0A8T7*PLUS, DNA-directed RNA polymerase #5: Protein | | Mass: 10249.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoZ, Z5075, ECs4524 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0A802, UniProt: P0A800*PLUS, DNA-directed RNA polymerase |
---|
-DNA chain , 2 types, 2 molecules PQ
#7: DNA chain | Mass: 19630.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
---|---|
#8: DNA chain | Mass: 19748.631 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
-Protein / RNA chain , 2 types, 2 molecules AR
#1: Protein | Mass: 130152.422 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: mfd, ACU57_04350, AUQ13_23175, BW690_23090, BZL31_08375, C5N07_18685, C9Z39_13430, CA593_22910, CI694_24470, CIG45_16475, D0X26_19775, D2185_03780, DAH34_08070, DBQ99_15575, E2119_09560, E4K55_ ...Gene: mfd, ACU57_04350, AUQ13_23175, BW690_23090, BZL31_08375, C5N07_18685, C9Z39_13430, CA593_22910, CI694_24470, CIG45_16475, D0X26_19775, D2185_03780, DAH34_08070, DBQ99_15575, E2119_09560, E4K55_21680, EAI52_08950, EEP23_04080, EI021_06895, EI028_16020, EIZ93_13025, EPT01_12285, EXX71_16985, EYD11_13865, F1E19_06650, FV293_24105, FWK02_07210, PGD_02181 Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A024L3Y3, UniProt: P30958*PLUS, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
---|---|
#6: RNA chain | Mass: 6815.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
-Non-polymers , 3 types, 5 molecules
#9: Chemical | ChemComp-ATP / | ||
---|---|---|---|
#10: Chemical | #11: Chemical | |
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Escherichia coli Mfd-RNA polymerase elongation complex: state II Type: COMPLEX / Entity ID: #1-#8 / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86000 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|