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 transcription reduction by a promoter-proximal +1 nucleosome.
Journal, issue, pages	Mol Cell, Vol. 83, Issue 11, Page 1798-11809.e7, Year 2023
Publish date	Jun 1, 2023
Authors	Julio Abril-Garrido / Christian Dienemann / Frauke Grabbe / Taras Velychko / Michael Lidschreiber / Haibo Wang / Patrick Cramer /
PubMed Abstract	At active human genes, the +1 nucleosome is located downstream of the RNA polymerase II (RNA Pol II) pre-initiation complex (PIC). However, at inactive genes, the +1 nucleosome is found further ...At active human genes, the +1 nucleosome is located downstream of the RNA polymerase II (RNA Pol II) pre-initiation complex (PIC). However, at inactive genes, the +1 nucleosome is found further upstream, at a promoter-proximal location. Here, we establish a model system to show that a promoter-proximal +1 nucleosome can reduce RNA synthesis in vivo and in vitro, and we analyze its structural basis. We find that the PIC assembles normally when the edge of the +1 nucleosome is located 18 base pairs (bp) downstream of the transcription start site (TSS). However, when the nucleosome edge is located further upstream, only 10 bp downstream of the TSS, the PIC adopts an inhibited state. The transcription factor IIH (TFIIH) shows a closed conformation and its subunit XPB contacts DNA with only one of its two ATPase lobes, inconsistent with DNA opening. These results provide a mechanism for nucleosome-dependent regulation of transcription initiation.
External links	Mol Cell / PubMed:37148879 / PubMed Central
Methods	EM (single particle)
Resolution	3.0 - 4.5 Å
Structure data	16274 8bvw EMDB-16274, PDB-8bvw: RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W) Method: EM (single particle) / Resolution: 4.0 Å 16331 8byq EMDB-16331, PDB-8byq: RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W) Method: EM (single particle) / Resolution: 4.1 Å 16335 8bz1 EMDB-16335, PDB-8bz1: RNA polymerase II core pre-initiation complex with the proximal +1 nucleosome (cPIC-Nuc10W) Method: EM (single particle) / Resolution: 3.8 Å EMDB-16336: RNA polymerase II core pre-initiation complex focused map Method: EM (single particle) / Resolution: 3.1 Å EMDB-16337: Proximal +1 nucleosome focused map Method: EM (single particle) / Resolution: 3.2 Å EMDB-16338: RNA polymerase II core pre-initiation complex with the proximal +1 nucleosome composite map Method: EM (single particle) / Resolution: 3.1 Å EMDB-16339: RNA polymerase II core pre-initiation complex focused map Method: EM (single particle) / Resolution: 3.2 Å EMDB-16340: Proximal +1 nucleosome focused map Method: EM (single particle) / Resolution: 3.2 Å EMDB-16341: TFIIH subcomplex CDK-activating kinase module focused map Method: EM (single particle) / Resolution: 3.8 Å EMDB-16342: General transcription factor IIH in closed conformation focused map Method: EM (single particle) / Resolution: 4.5 Å EMDB-16343: RNA polymerase II pre-initiation complex with the proximal +1 nucleosome composite map Method: EM (single particle) / Resolution: 3.4 Å EMDB-16365: RNA polymerase II core pre-initiation complex focused map Method: EM (single particle) / Resolution: 3.0 Å EMDB-16366: Distal +1 nucleosome focused map Method: EM (single particle) / Resolution: 3.6 Å EMDB-16367: General transcription factor IIH in open conformation focused map Method: EM (single particle) / Resolution: 4.3 Å EMDB-16368: TFIIH subcomplex CDK-activating kinase module focused map Method: EM (single particle) / Resolution: 3.3 Å EMDB-16369: RNA polymerase II pre-initiation complex with the distal +1 nucleosome composite map Method: EM (single particle) / Resolution: 3.2 Å
Chemicals	ChemComp-SF4: IRON/SULFUR CLUSTER / Iron–sulfur cluster ChemComp-ZN: Unknown entry ChemComp-MG: Unknown entry
Source	homo sapiens (human) sus scrofa (pig) xenopus laevis (African clawed frog) unidentified adenovirus pig (pig)
Keywords	TRANSCRIPTION / Mammalian PIC / +1 nucleosome / transcription initiation