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
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Journal
IF	>30 >20 >10 >5 all

Title	Structural basis of RfaH-mediated transcription-translation coupling.
Journal, issue, pages	Nat Struct Mol Biol, Vol. 31, Issue 12, Page 1932-1941, Year 2024
Publish date	Aug 8, 2024
Authors	Vadim Molodtsov / Chengyuan Wang / Jing Zhang / Jason T Kaelber / Gregor Blaha / Richard H Ebright /
PubMed Abstract	The NusG paralog RfaH mediates bacterial transcription-translation coupling in genes that contain a DNA sequence element, termed an ops site, required for pausing RNA polymerase (RNAP) and for ...The NusG paralog RfaH mediates bacterial transcription-translation coupling in genes that contain a DNA sequence element, termed an ops site, required for pausing RNA polymerase (RNAP) and for loading RfaH onto the paused RNAP. Here, we report cryo-electron microscopy structures of transcription-translation complexes (TTCs) containing Escherichia coli RfaH. The results show that RfaH bridges RNAP and the ribosome, with the RfaH N-terminal domain interacting with RNAP and the RfaH C-terminal domain interacting with the ribosome. The results show that the distribution of translational and orientational positions of RNAP relative to the ribosome in RfaH-coupled TTCs is more restricted than in NusG-coupled TTCs because of the more restricted flexibility of the RfaH interdomain linker. The results further suggest that the structural organization of RfaH-coupled TTCs in the 'loading state', in which RNAP and RfaH are located at the ops site during formation of the TTC, is the same as the structural organization of RfaH-coupled TTCs in the 'loaded state', in which RNAP and RfaH are located at positions downstream of the ops site during function of the TTC. The results define the structural organization of RfaH-containing TTCs and set the stage for analysis of functions of RfaH during translation initiation and transcription-translation coupling.
External links	Nat Struct Mol Biol / PubMed:39117885 / PubMed Central
Methods	EM (single particle)
Resolution	3.1 - 6.6 Å
Structure data	42453 8upo EMDB-42453, PDB-8upo: Escherichia coli transcription-translation coupled complex class A (TTC-A) containing RfaH bound to ops signal, mRNA with a 21 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome Method: EM (single particle) / Resolution: 5.5 Å 42454 8upr EMDB-42454, PDB-8upr: Escherichia coli transcription-translation coupled complex class A (TTC-A) containing RfaH bound to ops signal, mRNA with a 21 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome Method: EM (single particle) / Resolution: 5.3 Å 42473 8uql EMDB-42473, PDB-8uql: Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH in loaded state, mRNA with a 24 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome Method: EM (single particle) / Resolution: 3.2 Å 42474 8uqm EMDB-42474, PDB-8uqm: Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH in loaded state, NusA, mRNA with a 24 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome Method: EM (single particle) / Resolution: 5.3 Å 42477 8uqp EMDB-42477, PDB-8uqp: Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, mRNA with a 24 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome Method: EM (single particle) / Resolution: 3.8 Å 42479 8ur0 EMDB-42479, PDB-8ur0: Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, NusA, mRNA with a 24 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome Method: EM (single particle) / Resolution: 3.4 Å 42492 8urh EMDB-42492, PDB-8urh: Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, mRNA with a 27 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome Method: EM (single particle) / Resolution: 5.7 Å 42493 8uri EMDB-42493, PDB-8uri: Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, NusA, mRNA with a 27 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome Method: EM (single particle) / Resolution: 5.3 Å 42503 8urx EMDB-42503, PDB-8urx: Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, mRNA with a 30 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome Method: EM (single particle) / Resolution: 6.6 Å 42504 8ury EMDB-42504, PDB-8ury: Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, NusA, mRNA with a 30 nt long spacer, and fMet-tRNA in E-site and P-site of the ribosome Method: EM (single particle) / Resolution: 3.1 Å
Chemicals	ChemComp-MG: Unknown entry ChemComp-ZN: Unknown entry
Source	escherichia coli (E. coli) synthetic construct (others)
Keywords	TRANSCRIPTION / translation / RfaH / gene expression / regulation / ops / ribosome / coupling / expressome / NusA / RNA / RNA polymerase