9MU6 | pdb_00009mu6

Structure of native Drosophila melanogaster DLST

• PDB DOI: https://doi.org/10.2210/pdb9MU6/pdb
• EM Map EMD-48621: EMDB EMDataResource

• Classification: GENE REGULATION
• Organism(s): Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2025-01-13 Released: 2025-02-19 
• Deposition Author(s): 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.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.66 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Structural Characterization of Native RNA Polymerase II Transcription Complexes and Nucleosomes in Drosophila melanogaster.

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.

(2026) Nat Commun 17

• PubMed: 42711332 
• DOI: https://doi.org/10.1038/s41467-026-75963-0
• Primary Citation Related Structures: 
  9MU4, 9MU5, 9MU6, 9MU7, 9MU8, 9MU9


• 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.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, PA, USA.
Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, USA.
Center for Structural Biology, Pennsylvania State University, University Park, PA, USA.
Huck Institutes of Life Sciences, Pennsylvania State University, University Park, PA, USA.
Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
Department of Chemistry, Pennsylvania State University, University Park, PA, USA.
Department of Cell and Regenerative Biology, Wisconsin Blood Cancer Research Institute, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA.
Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA. [e-mail].
Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, PA, USA. [e-mail].
Center for Structural Biology, Pennsylvania State University, University Park, PA, USA. [e-mail].
Huck Institutes of Life Sciences, Pennsylvania State University, University Park, PA, USA. [e-mail].
Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA. [e-mail].
Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, USA. [e-mail].
Center for Structural Biology, Pennsylvania State University, University Park, PA, USA. [e-mail].
Huck Institutes of Life Sciences, Pennsylvania State University, University Park, PA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Octahedral - O  (Explore in 3D)
Global Stoichiometry: Homo 24-mer - A24 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 618.14 kDa 
• Atom Count: 43,134 
• Modeled Residue Count: 5,616 
• Deposited Residue Count: 5,616 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	234	Drosophila melanogaster	Mutation(s): 0  EC: 2.3.1.61
UniProt
Find proteins for Q9VGQ1 (Drosophila melanogaster) Explore Q9VGQ1  Go to UniProtKB:  Q9VGQ1

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.66 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.3.1
MODEL REFINEMENT	Coot	0.9.8.7
MODEL REFINEMENT	PHENIX	1.21.5207

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-02-19 
Deposition Author(s): 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.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM131860
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM047477
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM098399

Revision History  

• Version 1.0: 2025-02-19
  Type: Initial release
  
• Version 1.1: 2026-08-12
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2026-09-23
  Changes: Data collection, Database references