9MU4 | pdb_00009mu4

Structure of a native Drosophila melanogaster octameric nucleosome

PDB DOI: https://doi.org/10.2210/pdb9MU4/pdb
NAKB: 9MU4
EM Map EMD-48619: 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.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.29 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental, in silico
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

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

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.

To be published.

Macromolecule Content

Total Structure Weight: 188.36 kDa
Atom Count: 12,794
Modeled Residue Count: 1,098
Deposited Residue Count: 1,098
Unique protein chains: 4
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	A [auth c], B [auth g]	106	Drosophila melanogaster	Mutation(s): 0
UniProt
Find proteins for P84051 (Drosophila melanogaster) Explore P84051 Go to UniProtKB: P84051
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P84051
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B	C [auth d], D [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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02283
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	E [auth a], F [auth e]	100	Drosophila melanogaster	Mutation(s): 0
UniProt
Find proteins for P02299 (Drosophila melanogaster) Explore P02299 Go to UniProtKB: P02299
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02299
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	G [auth b], H [auth f]	82	Drosophila melanogaster	Mutation(s): 0
UniProt
Find proteins for P84040 (Drosophila melanogaster) Explore P84040 Go to UniProtKB: P84040
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P84040
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (164-MER)	I [auth T]	164	Drosophila melanogaster
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (164-MER)	J [auth N]	164	Drosophila melanogaster
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.29 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

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

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