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 of σ displacement and promoter escape in bacterial transcription.
Journal, issue, pages	Proc Natl Acad Sci U S A, Vol. 121, Issue 2, Page e2309670120, Year 2024
Publish date	Jan 9, 2024
Authors	Forson Gao / Fuzhou Ye / Bowen Zhang / Nora Cronin / Martin Buck / Xiaodong Zhang /
PubMed Abstract	Gene transcription is a fundamental cellular process carried out by RNA polymerase (RNAP). Transcription initiation is highly regulated, and in bacteria, transcription initiation is mediated by sigma ...Gene transcription is a fundamental cellular process carried out by RNA polymerase (RNAP). Transcription initiation is highly regulated, and in bacteria, transcription initiation is mediated by sigma (σ) factors. σ recruits RNAP to the promoter DNA region, located upstream of the transcription start site (TSS) and facilitates open complex formation, where double-stranded DNA is opened up into a transcription bubble and template strand DNA is positioned inside RNAP for initial RNA synthesis. During initial transcription, RNAP remains bound to σ and upstream DNA, presumably with an enlarging transcription bubble. The release of RNAP from upstream DNA is required for promoter escape and processive transcription elongation. Bacteria sigma factors can be broadly separated into two classes with the majority belonging to the σ class, represented by the σ that regulates housekeeping genes. σ forms a class on its own and regulates stress response genes. Extensive studies on σ have revealed the molecular mechanisms of the σ dependent process while how σ transitions from initial transcription to elongation is currently unknown. Here, we present a series of cryo-electron microscopy structures of the RNAP-σ initial transcribing complexes with progressively longer RNA, which reveal structural changes that lead to promoter escape. Our data show that initially, the transcription bubble enlarges, DNA strands scrunch, reducing the interactions between σ and DNA strands in the transcription bubble. RNA extension and further DNA scrunching help to release RNAP from σ and upstream DNA, enabling the transition to elongation.
External links	Proc Natl Acad Sci U S A / PubMed:38170755 / PubMed Central
Methods	EM (single particle)
Resolution	2.8 - 3.9 Å
Structure data	19079 8re4 EMDB-19079, PDB-8re4: Cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 5nt pre-translocated complex Method: EM (single particle) / Resolution: 2.8 Å 19080 8rea EMDB-19080, PDB-8rea: Cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 5nt post-translocated complex Method: EM (single particle) / Resolution: 3.4 Å 19081 8reb EMDB-19081, PDB-8reb: Cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 6nt complex Method: EM (single particle) / Resolution: 3.4 Å 19082 8rec EMDB-19082, PDB-8rec: Cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 7nt complex Method: EM (single particle) / Resolution: 3.5 Å 19083 8red EMDB-19083, PDB-8red: Cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 8nt complex Method: EM (single particle) / Resolution: 3.9 Å 19084 8ree EMDB-19084, PDB-8ree: Cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 9nt complex Method: EM (single particle) / Resolution: 3.8 Å
Chemicals	ChemComp-MG: Unknown entry ChemComp-ZN: Unknown entry
Source	escherichia coli k-12 (bacteria) klebsiella oxytoca (bacteria)
Keywords	TRANSCRIPTION / initiation / rna polymerase / sigma54