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	Single-stranded DNA drives σ subunit loading onto mycobacterial RNA polymerase to unlock initiation-competent conformations.
Journal, issue, pages	Nucleic Acids Res, Vol. 53, Issue 7, Year 2025
Publish date	Apr 10, 2025
Authors	Rishi Kishore Vishwakarma / Nils Marechal / Zakia Morichaud / Mickaël Blaise / Emmanuel Margeat / Konstantin Brodolin /
PubMed Abstract	Initiation of transcription requires the formation of the "open" promoter complex (RPo). For this, the σ subunit of bacterial RNA polymerase (RNAP) binds to the nontemplate strand of the -10 element ...Initiation of transcription requires the formation of the "open" promoter complex (RPo). For this, the σ subunit of bacterial RNA polymerase (RNAP) binds to the nontemplate strand of the -10 element sequence of promoters and nucleates DNA unwinding. This is accompanied by a cascade of conformational changes on RNAP, the exact mechanics of which remains elusive. Here, using single-molecule Förster resonance energy transfer and cryo-electron microscopy, we explored the conformational landscape of RNAP from the human pathogen Mycobacterium tuberculosis upon binding to a single-stranded DNA (ssDNA) fragment that includes the -10 element sequence (-10 ssDNA). We found that like the transcription activator RNAP-binding protein A, -10 ssDNA induced σ subunit loading onto the DNA/RNA channels of RNAP. This triggered RNAP clamp closure and unswiveling that are required for RPo formation and RNA synthesis initiation. Our results reveal a mechanism of ssDNA-guided RNAP maturation and identify the σ subunit as a regulator of RNAP conformational dynamics.
External links	Nucleic Acids Res / PubMed:40240004 / PubMed Central
Methods	EM (single particle)
Resolution	3.2 - 4.33 Å
Structure data	50508 9fjp EMDB-50508, PDB-9fjp: Cryo-EM structure of Mycobacterium tuberculosis sigma-B RNA polymerase bound to -10 promoter element ssDNA oligo Method: EM (single particle) / Resolution: 3.2 Å EMDB-50509: cryo-EM structure of Mycobacterium tuberculosis sigma-B RNA polymerase bound to -10 promoter element ssDNA oligo - consensus map Method: EM (single particle) / Resolution: 3.33 Å 50510 9fjr EMDB-50510, PDB-9fjr: Cryo-EM structure of Mycobacterium tuberculosis sigma-B RNA polymerase bound to -10 promoter element ssDNA oligo - sigma-B docked conformation Method: EM (single particle) / Resolution: 3.43 Å 50511 9fjs EMDB-50511: Cryo-EM structure of Mycobacterium tuberculosis sigma-B RNA polymerase bound to -10 promoter element ssDNA oligo - sigma-B udocked conformation PDB-9fjs: Cryo-EM structure of Mycobacterium tuberculosis sigma-B RNA polymerase bound to -10 promoter element ssDNA oligo - sigma-B undocked conformation Method: EM (single particle) / Resolution: 3.48 Å EMDB-50512: Cryo-EM structure of Mycobacterium tuberculosis sigma-B RNA polymerase bound to -10 promoter element ssDNA oligo - swiveled conformation Method: EM (single particle) / Resolution: 4.33 Å EMDB-50514: Cryo-EM structure of Mycobacterium tuberculosis sigma-B RNA polymerase bound to -10 promoter element ssDNA oligo - unswiveled conformation Method: EM (single particle) / Resolution: 3.79 Å
Chemicals	ChemComp-ZN: Unknown entry ChemComp-MG: Unknown entry
Source	mycobacterium tuberculosis h37rv (bacteria) escherichia coli (E. coli)
Keywords	TRANSCRIPTION / RNA polymerase; sigma factor; SigB / stress response; -10 promoter element; promoter recognition; tuberculosis