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	Structures of mammalian RNA polymerase II pre-initiation complexes.
Journal, issue, pages	Nature, Vol. 594, Issue 7861, Page 124-128, Year 2021
Publish date	Apr 26, 2021
Authors	Shintaro Aibara / Sandra Schilbach / Patrick Cramer /
PubMed Abstract	The initiation of transcription is a focal point for the regulation of gene activity during mammalian cell differentiation and development. To initiate transcription, RNA polymerase II (Pol II) ...The initiation of transcription is a focal point for the regulation of gene activity during mammalian cell differentiation and development. To initiate transcription, RNA polymerase II (Pol II) assembles with general transcription factors into a pre-initiation complex (PIC) that opens promoter DNA. Previous work provided the molecular architecture of the yeast and human PIC and a topological model for DNA opening by the general transcription factor TFIIH. Here we report the high-resolution cryo-electron microscopy structure of PIC comprising human general factors and Sus scrofa domesticus Pol II, which is 99.9% identical to human Pol II. We determine the structures of PIC with closed and opened promoter DNA at 2.5-2.8 Å resolution, and resolve the structure of TFIIH at 2.9-4.0 Å resolution. We capture the TFIIH translocase XPB in the pre- and post-translocation states, and show that XPB induces and propagates a DNA twist to initiate the opening of DNA approximately 30 base pairs downstream of the TATA box. We also provide evidence that DNA opening occurs in two steps and leads to the detachment of TFIIH from the core PIC, which may stop DNA twisting and enable RNA chain initiation.
External links	Nature / PubMed:33902107
Methods	EM (single particle)
Resolution	2.4 - 9.1 Å
Structure data	12610 7nvr EMDB-12610, PDB-7nvr: Human Mediator with RNA Polymerase II Pre-initiation complex Method: EM (single particle) / Resolution: 4.5 Å 12611 7nvs EMDB-12611, PDB-7nvs: RNA polymerase II core pre-initiation complex with closed promoter DNA in proximal position Method: EM (single particle) / Resolution: 2.8 Å 12612 7nvt EMDB-12612, PDB-7nvt: RNA polymerase II core pre-initiation complex with closed promoter DNA in distal position Method: EM (single particle) / Resolution: 2.9 Å 12613 7nvu EMDB-12613, PDB-7nvu: RNA polymerase II core pre-initiation complex with open promoter DNA Method: EM (single particle) / Resolution: 2.5 Å 12614 7nvv EMDB-12614, PDB-7nvv: XPB-containing part of TFIIH in a post-translocated state (with ADP-BeF3) Method: EM (single particle) / Resolution: 2.9 Å 12615 7nvw EMDB-12615, PDB-7nvw: TFIIH in a pre-translocated state (without ADP-BeF3) Method: EM (single particle) / Resolution: 4.3 Å 12616 7nvx EMDB-12616, PDB-7nvx: TFIIH in a post-translocated state (with ADP-BeF3) Method: EM (single particle) / Resolution: 3.9 Å 12617 7nvy EMDB-12617, PDB-7nvy: RNA polymerase II pre-initiation complex with closed promoter DNA in proximal position Method: EM (single particle) / Resolution: 7.3 Å 12618 7nvz EMDB-12618, PDB-7nvz: RNA polymerase II pre-initiation complex with closed promoter DNA in distal position Method: EM (single particle) / Resolution: 7.2 Å 12619 7nw0 EMDB-12619, PDB-7nw0: RNA polymerase II pre-initiation complex with open promoter DNA Method: EM (single particle) / Resolution: 6.6 Å EMDB-12620: Focused refinement of the core RNA polymerase II pre-initiation complex in a consensus CC state (without ADP-BeF3) Method: EM (single particle) / Resolution: 2.4 Å EMDB-12621: Focused refinement of the core RNA polymerase II pre-initiation complex in a consensus OC state (with ADP-BeF3) Method: EM (single particle) / Resolution: 2.4 Å EMDB-12622: Focused refinement of the upstream complex for the RNA polymerase II pre-initiation complex in a consensus CC state (without ADP-BeF3) Method: EM (single particle) / Resolution: 2.8 Å EMDB-12623: Focused refinement of the upstream complex for the RNA polymerase II pre-initiation complex in a consensus OC state (with ADP-BeF3) Method: EM (single particle) / Resolution: 2.7 Å EMDB-12624: Focused refinement of XPB containing part of TFIIH in pre-translocated state (without ADP-BeF3) Method: EM (single particle) / Resolution: 3.3 Å EMDB-12625: Focused refinement of XPD containing part of TFIIH in pre-translocated state (without ADP-BeF3) Method: EM (single particle) / Resolution: 4.1 Å EMDB-12626: Focused refinement of XPD containing part of TFIIH in post-translocated state (with ADP-BeF3) Method: EM (single particle) / Resolution: 4.0 Å EMDB-12627: Focused refinement of the RNA polymerase II core pre-initiation complex in a consensus IC-like state (with ADP-BeF3) Method: EM (single particle) / Resolution: 2.4 Å EMDB-12628: Focused refinement of the upstream complex for the RNA polymerase II pre-initiation complex in a consensus IC-like state (with ADP-BeF3) Method: EM (single particle) / Resolution: 2.7 Å EMDB-12629: Focused refinement of the core RNA polymerase II pre-initiation complex with intermediary promoter DNA (with ADP-BeF3) Method: EM (single particle) / Resolution: 2.8 Å EMDB-12630: RNA polymerase II pre-initiation complex with intermediary promoter DNA Method: EM (single particle) / Resolution: 9.1 Å
Chemicals	ChemComp-SF4: IRON/SULFUR CLUSTER / Iron–sulfur cluster ChemComp-ZN: Unknown entry ChemComp-MG: Unknown entry ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM / Adenosine diphosphate ChemComp-BEF*: BERYLLIUM TRIFLUORIDE ION
Source	homo sapiens (human) sus scrofa (pig) human mastadenovirus c trichoplusia ni (cabbage looper) Pig (pig) unidentified adenovirus
Keywords	TRANSCRIPTION / Mediator complex / RNA polymerase II / TFIIH / Pre-initiation complex / Initiation