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	Three-step mechanism of promoter escape by RNA polymerase II.
Journal, issue, pages	Mol Cell, Year 2024
Publish date	Apr 5, 2024
Authors	Yumeng Zhan / Frauke Grabbe / Elisa Oberbeckmann / Christian Dienemann / Patrick Cramer /
PubMed Abstract	The transition from transcription initiation to elongation is highly regulated in human cells but remains incompletely understood at the structural level. In particular, it is unclear how ...The transition from transcription initiation to elongation is highly regulated in human cells but remains incompletely understood at the structural level. In particular, it is unclear how interactions between RNA polymerase II (RNA Pol II) and initiation factors are broken to enable promoter escape. Here, we reconstitute RNA Pol II promoter escape in vitro and determine high-resolution structures of initially transcribing complexes containing 8-, 10-, and 12-nt ordered RNAs and two elongation complexes containing 14-nt RNAs. We suggest that promoter escape occurs in three major steps. First, the growing RNA displaces the B-reader element of the initiation factor TFIIB without evicting TFIIB. Second, the rewinding of the transcription bubble coincides with the eviction of TFIIA, TFIIB, and TBP. Third, the binding of DSIF and NELF facilitates TFIIE and TFIIH dissociation, establishing the paused elongation complex. This three-step model for promoter escape fills a gap in our understanding of the initiation-elongation transition of RNA Pol II transcription.
External links	Mol Cell / PubMed:38604172
Methods	EM (single particle)
Resolution	2.9 - 7.4 Å
Structure data	19718 8s51 EMDB-19718, PDB-8s51: RNA polymerase II core initially transcribing complex with an ordered RNA of 8 nt Method: EM (single particle) / Resolution: 3.1 Å 19719 8s52 EMDB-19719, PDB-8s52: RNA polymerase II core initially transcribing complex with an ordered RNA of 10 nt Method: EM (single particle) / Resolution: 2.9 Å 19720 8s54 EMDB-19720, PDB-8s54: RNA polymerase II early elongation complex bound to TFIIE and TFIIF - state b (composite structure) Method: EM (single particle) / Resolution: 3.4 Å EMDB-19721: RNA polymerase II initially transcribing complex with an ordered RNA of 8 nt Method: EM (single particle) / Resolution: 3.9 Å EMDB-19722: RNA polymerase II initially transcribing complex with an ordered RNA of 10 nt Method: EM (single particle) / Resolution: 3.5 Å EMDB-19723: RNA polymerase II initially transcribing complex with an ordered RNA of 12 nt Method: EM (single particle) / Resolution: 7.4 Å EMDB-19724: RNA polymerase II early elongation complex bound to TFIIE, TFIIF and TFIIH - state a Method: EM (single particle) / Resolution: 6.0 Å EMDB-19725: RNA polymerase II early elongation complex bound to TFIIE, TFIIF and TFIIH - state b Method: EM (single particle) / Resolution: 6.2 Å 19726 8s55 EMDB-19726, PDB-8s55: RNA polymerase II early elongation complex bound to TFIIE and TFIIF - state a (composite structure) Method: EM (single particle) / Resolution: 3.4 Å 19743 8s5n EMDB-19743, PDB-8s5n: RNA polymerase II core initially transcribing complex with an ordered RNA of 12 nt Method: EM (single particle) / Resolution: 3.4 Å EMDB-19795: RNA polymerase II early elongation complex bound to TFIIE and TFIIF - state a (global map) Method: EM (single particle) / Resolution: 3.4 Å EMDB-19796: RNA polymerase II early elongation complex bound to TFIIE and TFIIF - state b (global map) Method: EM (single particle) / Resolution: 3.3 Å EMDB-19797: EC14 core Pol II focused map Method: EM (single particle) / Resolution: 3.4 Å
Chemicals	ChemComp-ZN: Unknown entry ChemComp-MG: Unknown entry
Source	sus scrofa (pig) unidentified adenovirus homo sapiens (human)
Keywords	TRANSCRIPTION / RNA polymerase II / promoter escape / de novo initiation / de novo transcription