Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structural basis for transcription complex disruption by the Mfd translocase.
Journal, issue, pages	Elife, Vol. 10, Year 2021
Publish date	Jan 22, 2021
Authors	Jin Young Kang / Eliza Llewellyn / James Chen / Paul Dominic B Olinares / Joshua Brewer / Brian T Chait / Elizabeth A Campbell / Seth A Darst /
PubMed 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.
External links	Elife / PubMed:33480355 / PubMed Central
Methods	EM (single particle)
Resolution	3.3 - 4.1 Å
Structure data	21996 6x26 EMDB-21996, PDB-6x26: Mfd-bound E.coli RNA polymerase elongation complex - L1 state Method: EM (single particle) / Resolution: 4.1 Å 22006 6x2f EMDB-22006, PDB-6x2f: Mfd-bound E.coli RNA polymerase elongation complex - L2 state Method: EM (single particle) / Resolution: 4.0 Å 22012 6x2n EMDB-22012, PDB-6x2n: Mfd-bound E.coli RNA polymerase elongation complex - I state Method: EM (single particle) / Resolution: 3.9 Å 22039 6x43 EMDB-22039, PDB-6x43: Mfd-bound E.coli RNA polymerase elongation complex - II state Method: EM (single particle) / Resolution: 3.6 Å 22043 6x4w EMDB-22043, PDB-6x4w: Mfd-bound E.coli RNA polymerase elongation complex - III state Method: EM (single particle) / Resolution: 3.8 Å 22044 6x4y EMDB-22044, PDB-6x4y: Mfd-bound E.coli RNA polymerase elongation complex - IV state Method: EM (single particle) / Resolution: 3.6 Å 22045 6x50 EMDB-22045, PDB-6x50: Mfd-bound E.coli RNA polymerase elongation complex - V state Method: EM (single particle) / Resolution: 3.3 Å
Chemicals	ChemComp-MG: Unknown entry ChemComp-ZN: Unknown entry ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM / Adenosine diphosphate ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying moleculeYM / Adenosine triphosphate
Source	escherichia coli (E. coli)
Keywords	TRANSCRIPTION/RNA/DNA / Transcription-coupled DNA repair / DNA translocase / elongation complex / RNA polymerase / TRANSCRIPTION / TRANSCRIPTION-RNA-DNA complex