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 visualization of transcription activated by a multidrug-sensing MerR family regulator.
Journal, issue, pages	Nat Commun, Vol. 12, Issue 1, Page 2702, Year 2021
Publish date	May 11, 2021
Authors	Yang Yang / Chang Liu / Wei Zhou / Wei Shi / Ming Chen / Baoyue Zhang / David G Schatz / Yangbo Hu / Bin Liu /
PubMed Abstract	Bacterial RNA polymerase (RNAP) holoenzyme initiates transcription by recognizing the conserved -35 and -10 promoter elements that are optimally separated by a 17-bp spacer. The MerR family of ...Bacterial RNA polymerase (RNAP) holoenzyme initiates transcription by recognizing the conserved -35 and -10 promoter elements that are optimally separated by a 17-bp spacer. The MerR family of transcriptional regulators activate suboptimal 19-20 bp spacer promoters in response to myriad cellular signals, ranging from heavy metals to drug-like compounds. The regulation of transcription by MerR family regulators is not fully understood. Here we report one crystal structure of a multidrug-sensing MerR family regulator EcmrR and nine cryo-electron microscopy structures that capture the EcmrR-dependent transcription process from promoter opening to initial transcription to RNA elongation. These structures reveal that EcmrR is a dual ligand-binding factor that reshapes the suboptimal 19-bp spacer DNA to enable optimal promoter recognition, sustains promoter remodeling to stabilize initial transcribing complexes, and finally dissociates from the promoter to reverse DNA remodeling and facilitate the transition to elongation. Our findings yield a comprehensive model for transcription regulation by MerR family factors and provide insights into the transition from transcription initiation to elongation.
External links	Nat Commun / PubMed:33976201 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	1.4 - 3.3 Å
Structure data	22234 6xl5 EMDB-22234, PDB-6xl5: Cryo-EM structure of EcmrR-RNAP-promoter open complex (EcmrR-RPo) Method: EM (single particle) / Resolution: 2.5 Å 22235 6xl6 EMDB-22235, PDB-6xl6: Cryo-EM structure of EcmrR-DNA complex in EcmrR-RPo Method: EM (single particle) / Resolution: 3.0 Å 22236 6xl9 EMDB-22236, PDB-6xl9: Cryo-EM structure of EcmrR-RNAP-promoter initial transcribing complex with 3-nt RNA transcript (EcmrR-RPitc-3nt) Method: EM (single particle) / Resolution: 2.5 Å 22237 6xla EMDB-22237, PDB-6xla: Cryo-EM structure of EcmrR-DNA complex in EcmrR-RPitc-3nt Method: EM (single particle) / Resolution: 3.1 Å 22245 6xlj EMDB-22245, PDB-6xlj: Cryo-EM structure of EcmrR-RNAP-promoter initial transcribing complex with 4-nt RNA transcript (EcmrR-RPitc-4nt) Method: EM (single particle) / Resolution: 2.7 Å 22246 6xlk EMDB-22246, PDB-6xlk: Cryo-EM structure of EcmrR-DNA complex in EcmrR-RPitc-4nt Method: EM (single particle) / Resolution: 3.3 Å 22247 6xll EMDB-22247, PDB-6xll: Cryo-EM structure of E. coli RNAP-promoter initial transcribing complex with 5-nt RNA transcript (RPitc-5nt) Method: EM (single particle) / Resolution: 2.7 Å 22248 6xlm EMDB-22248, PDB-6xlm: Cryo-EM structure of E.coli RNAP-DNA elongation complex 1 (RDe1) in EcmrR-dependent transcription Method: EM (single particle) / Resolution: 3.2 Å 22249 6xln EMDB-22249, PDB-6xln: Cryo-EM structure of E. coli RNAP-DNA elongation complex 2 (RDe2) in EcmrR-dependent transcription Method: EM (single particle) / Resolution: 2.8 Å EMDB-23291: Cryo-EM map of EcmrR-RNAP-promoter open complex (EcmrR-RPo) with clear NCR-EcmrR NTD interface density Method: EM (single particle) / Resolution: 2.9 Å PDB-6wl5: Crystal structure of EcmrR C-terminal domain Method: X-RAY DIFFRACTION / Resolution: 1.4 Å
Chemicals	ChemComp-16A: CETYL-TRIMETHYL-AMMONIUM ChemComp-GOL: GLYCEROL ChemComp-CL: Unknown entry ChemComp-EDO: 1,2-ETHANEDIOL ChemComp-HOH: WATER ChemComp-1N7: CHAPSO / detergentYM ChemComp-MG: Unknown entry ChemComp-ZN: Unknown entry ChemComp-118*: TETRAPHENYLANTIMONIUM ION
Source	escherichia coli o157:h7 (bacteria) escherichia coli (E. coli)
Keywords	TRANSCRIPTION / Transcriptional factor / TRANSFERASE/DNA / TRANSFERASE-DNA complex / promoter / multidrug recognition / TRANSCRIPTION TRANSFERASE-DNA complex / promoter escape