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	The +1 nucleosome functions in RNA Pol II transcription initiation and the transition to elongation.
Journal, issue, pages	Mol Cell, Vol. 86, Issue 15, Page 2939-22949.e7, Year 2026
Publish date	Aug 6, 2026
Authors	Yumeng Zhan / Julio Abril-Garrido / Frauke Grabbe / Paulina Seweryn / Ute Neef / Christian Dienemann / Patrick Cramer /
PubMed Abstract	Transcription initiation by RNA polymerase II (RNA Pol II) occurs next to a +1 nucleosome, which is positioned downstream of the transcription start site (TSS). The +1 nucleosome influences pre- ...Transcription initiation by RNA polymerase II (RNA Pol II) occurs next to a +1 nucleosome, which is positioned downstream of the transcription start site (TSS). The +1 nucleosome influences pre-initiation complex (PIC) assembly and RNA Pol II pausing, but its function in transcription initiation and the transition to elongation remains unclear. Here, we investigate the transcription initiation-elongation transition in vitro using DNA templates containing a +1 nucleosome and present cryo-electron microscopy (cryo-EM) structures of five intermediate states. First, after PIC assembly, ATP binding to TFIIH enables the +1 nucleosome to evict TFIID from the PIC. Following DNA opening, the +1 nucleosome stimulates TFIIH translocase activity and initial RNA synthesis. Finally, after DNA bubble rewinding, the +1 nucleosome removes TFIIH from the early elongation complex for promoter escape. Our findings show that the +1 nucleosome not only acts passively in PIC assembly and RNA Pol II pausing but rather has active functions during the initiation-elongation transition of transcription.
External links	Mol Cell / PubMed:42480520
Methods	EM (single particle)
Resolution	3.1 - 12.4 Å
Structure data	57364 29tk EMDB-57364, PDB-29tk: RNA polymerase II elongation complex with the +1 nucleosome Method: EM (single particle) / Resolution: 3.9 Å EMDB-57365: Consensus map for RNA Polymerase II elongation complex with the +1 nucleosome Method: EM (single particle) / Resolution: 3.9 Å 57390 29vf EMDB-57390, PDB-29vf: RNA polymerase II initially transcribing complex with a 2-nt RNA and the +1 nucleosome Method: EM (single particle) / Resolution: 7.5 Å EMDB-57391: Focused refinement map of core Pol II Method: EM (single particle) / Resolution: 3.27 Å EMDB-57392: Focused refinement map of nucleosome in RNA polymerase II elongation complex with the +1 nucleosome Method: EM (single particle) / Resolution: 3.71 Å EMDB-57394: Focused refinement map of nucleosome of RNA polymerase II initially transcribing complex with a 2-nt RNA and the +1 nucleosome Method: EM (single particle) / Resolution: 7.2 Å EMDB-57395: Focused refinement map of cPIC of RNA polymerase II initially transcribing complex with a 2-nt RNA and the +1 nucleosome Method: EM (single particle) / Resolution: 4.26 Å 57401 29wd EMDB-57401: RNA polymerase II pre-initiation complex bound to ADP-BeF3 in the presence of the +1 nucleosome PDB-29wd: RNA polymerase II initially transcribing complex with a 2-nt RNA and the +1 nucleosome Method: EM (single particle) / Resolution: 4.2 Å EMDB-57402: Focused refinement map of the nucleosome in RNA polymerase II pre-initiation complex bound to ADP-BeF3 in the presence of the +1 nucleosome Method: EM (single particle) / Resolution: 4.1 Å EMDB-57403: focused refinement map of core PIC in RNA polymerase II pre-initiation complex bound to ADP-BeF3 in the presence of the +1 nucleosome Method: EM (single particle) / Resolution: 3.6 Å EMDB-57406: Focused refinement map of TFIIH in RNA polymerase II pre-initiation complex bound to ADP-BeF3 in the presence of the +1 nucleosome Method: EM (single particle) / Resolution: 4.2 Å EMDB-57407: Focused refinement map of XPB in RNA polymerase II pre-initiation complex bound to ADP-BeF3 in the presence of the +1 nucleosome Method: EM (single particle) / Resolution: 3.1 Å EMDB-57541: Focused map of the +1 nucleosome (Closed complex) Method: EM (single particle) / Resolution: 7.5 Å EMDB-57544: Focused map of core RNA polymerase II pre-initiation complex (PIC) (Closed complex) Method: EM (single particle) / Resolution: 4.4 Å EMDB-57545: Focused map of general transcription factor IIH (Closed complex) Method: EM (single particle) / Resolution: 11.1 Å EMDB-57628: Focused map of transcription initiation factor IID (TFIID) (Closed complex) Method: EM (single particle) / Resolution: 12.4 Å 57691 30ff EMDB-57691, PDB-30ff: TFIID-containing RNA polymerase II pre-initiation complex in the presence of the +1 nucleosome Method: EM (single particle) / Resolution: 8.5 Å 57693 30fh EMDB-57693, PDB-30fh: RNA polymerase II initially transcribing complex with a 6-nt RNA and the +1 nucleosome Method: EM (single particle) / Resolution: 7.6 Å EMDB-57789: Focused map of the +1 nucleosome (ITC6) Method: EM (single particle) / Resolution: 4.0 Å EMDB-57793: Focused map of general transcription factor IIH (ITC6) Method: EM (single particle) / Resolution: 9.0 Å EMDB-57807: Focused map of core RNA polymerase II pre-initiation complex (PIC) (ITC6) Method: EM (single particle) / Resolution: 3.4 Å
Chemicals	ChemComp-ZN: Unknown entry ChemComp-MG: Unknown entry ChemComp-SF4: IRON/SULFUR CLUSTER ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM ChemComp-BEF: BERYLLIUM TRIFLUORIDE ION ChemComp-UNK: UNKNOWN ChemComp-2A1: (2S)-2-aminopropan-1-ol ChemComp-ALA*: ALANINE
Source	homo sapiens (human) sus scrofa (pig) xenopus laevis (African clawed frog) unidentified adenovirus synthetic construct (others)
Keywords	TRANSCRIPTION / RNA polymerase II / Mammalian PIC / +1 nucleosome / transcription initiation