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 Characterization of Native RNA Polymerase II Transcription Complexes and Nucleosomes in Drosophila melanogaster.
Journal, issue, pages	Nat Commun, Vol. 17, Issue 1, Year 2026
Publish date	Aug 5, 2026
Authors	Natalie L Venette-Smith / Rishi K Vishwakarma / Varun Venkatakrishnan / Roberta Dollinger / Josie Schultz / Paul Babitzke / Ganesh Anand / David S Gilmour / Jean-Paul Armache / Katsuhiko S Murakami /
PubMed Abstract	Structural studies of eukaryotic RNA polymerase II (Pol II) transcription often rely on in vitro assembly, which may not fully represent native conditions. To investigate Pol II transcription in ...Structural studies of eukaryotic RNA polymerase II (Pol II) transcription often rely on in vitro assembly, which may not fully represent native conditions. To investigate Pol II transcription in metazoan cells, we developed a method to isolate native transcription complexes from Drosophila melanogaster embryos using FLAG-tag affinity purification and Micrococcal Nuclease treatment. Cryo-EM and proteomics studies revealed diverse transcription complexes and nucleosomes, including a metazoan Rpb4/Rpb7 stalk-less Pol II elongation complex and a hexameric nucleosome lacking an H2A/H2B dimer. Notably, nucleosome is found only downstream of the nucleosome elongation complex, underscoring it as a major energy barrier and a time-consuming step during Pol II progression through chromatin. Proteomics identified co-purified factors involved in transcription initiation, elongation, and RNA modification. This study provides a framework for investigations of transcription in cells, paving the way for future studies of transient and minor complexes.
External links	Nat Commun / PubMed:42711332 / PubMed Central
Methods	EM (single particle)
Resolution	2.86 - 7.8 Å
Structure data	48619 9mu4 EMDB-48619, PDB-9mu4: Structure of a native Drosophila melanogaster octameric nucleosome Method: EM (single particle) / Resolution: 3.29 Å 48620 9mu5 EMDB-48620, PDB-9mu5: Structure of a native Drosophila melanogaster hexameric nucleosome Method: EM (single particle) / Resolution: 6.3 Å 48621 9mu6 EMDB-48621, PDB-9mu6: Structure of native Drosophila melanogaster DLST Method: EM (single particle) / Resolution: 3.66 Å 48622 9mu7 EMDB-48622, PDB-9mu7: Structure of a native Drosophila melanogaster Pol II Elongation Complex with a well-defined Rpb4/Rpb7 stalk Method: EM (single particle) / Resolution: 3.44 Å 48623 9mu8 EMDB-48623, PDB-9mu8: Structure of a native Drosophila melanogaster Pol II Elongation Complex without Rpb4/Rpb7 stalk Method: EM (single particle) / Resolution: 3.37 Å EMDB-48624: Structure of a native Drosophila melanogaster Pol II Elongation Complex Method: EM (single particle) / Resolution: 2.86 Å 48626 9mu9 EMDB-48626, PDB-9mu9: Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Composite map Method: EM (single particle) / Resolution: 7.8 Å EMDB-48823: Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Focused refinement of nucleosome Method: EM (single particle) / Resolution: 6.12 Å EMDB-48829: Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Focused refinement of Pol II Method: EM (single particle) / Resolution: 4.31 Å
Chemicals	ChemComp-ZN: Unknown entry
Source	drosophila melanogaster (fruit fly)
Keywords	GENE REGULATION / Nucleosome / histones / histone / chromatin / DNA / succinyltransferase / DLST / TRANSCRIPTION / polymerase / Pol II / mRNA