9MU4

Structure of a native Drosophila melanogaster octameric nucleosome

Summary for 9MU4

• Entry DOI: 10.2210/pdb9mu4/pdb
• EMDB information: 48619
• Descriptor: Histone H2A, Histone H2B, Histone H3, ... (6 entities in total)
• Functional Keywords: nucleosome, histones, histone, chromatin, dna, gene regulation
• Biological source: Drosophila melanogaster (fruit fly); More
• Total number of polymer chains: 10
• Total formula weight: 188360.39

Authors

Venette-Smith, N.L.,Vishwakarma, R.K.,Dollinger, R.,Schultz, J.,Venkatakrishnan, V.,Babitzke, P.,Anand, G.,Gilmour, D.S.,Armache, J.-P.,Murakami, K.S. (deposition date: 2025-01-13, release date: 2025-02-19, Last modification date: 2026-09-23)

Primary citation

Venette-Smith, N.L.,Vishwakarma, R.K.,Venkatakrishnan, V.,Dollinger, R.,Schultz, J.,Babitzke, P.,Anand, G.,Gilmour, D.S.,Armache, J.P.,Murakami, K.S.
Structural Characterization of Native RNA Polymerase II Transcription Complexes and Nucleosomes in Drosophila melanogaster.
Nat Commun, 17:-, 2026

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 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.

PubMed: 42711332
DOI: 10.1038/s41467-026-75963-0

Experimental method

ELECTRON MICROSCOPY (3.29 Å)