9MU5 | pdb_00009mu5

Structure of a native Drosophila melanogaster hexameric nucleosome

PDB DOI: https://doi.org/10.2210/pdb9MU5/pdb
NAKB: 9MU5
EM Map EMD-48620: 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)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 6.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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

DOI: https://doi.org/10.1038/s41467-026-75963-0

Macromolecule Content

Total Structure Weight: 143.99 kDa
Atom Count: 9,666
Modeled Residue Count: 798
Deposited Residue Count: 812
Unique protein chains: 4
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	A [auth g]	105	Drosophila melanogaster	Mutation(s): 0
UniProt
Find proteins for P84051 (Drosophila melanogaster) Explore P84051 Go to UniProtKB: P84051
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P84051
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B	B [auth h]	97	Drosophila melanogaster	Mutation(s): 0
UniProt
Find proteins for P02283 (Drosophila melanogaster) Explore P02283 Go to UniProtKB: P02283
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02283
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	C [auth a], D [auth e]	92	Drosophila melanogaster	Mutation(s): 0
UniProt
Find proteins for P02299 (Drosophila melanogaster) Explore P02299 Go to UniProtKB: P02299
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02299
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	E [auth b], F [auth f]	80	Drosophila melanogaster	Mutation(s): 0
UniProt
Find proteins for P84040 (Drosophila melanogaster) Explore P84040 Go to UniProtKB: P84040
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P84040
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 5
DNA (133-MER)	G [auth N]	133	Drosophila melanogaster
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 6
DNA (133-MER)	H [auth T]	133	Drosophila melanogaster
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 6.30 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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-02-19

Deposition Author(s):

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