9MU9 | pdb_00009mu9

Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Composite map

PDB DOI: https://doi.org/10.2210/pdb9MU9/pdb
NAKB: 9MU9
EM Map EMD-48626: EMDB EMDataResource

Classification: TRANSCRIPTION
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: 7.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

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: 615.73 kDa
Atom Count: 42,423
Modeled Residue Count: 4,793
Deposited Residue Count: 4,802
Unique protein chains: 14
Unique nucleic acid chains: 3

Macromolecules

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	D [auth g], E [auth c]	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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B	F [auth h], G [auth d]	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
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	H [auth e], I [auth a]	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
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	J [auth f], K [auth b]	80	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
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB1	L [auth A]	1,470	Drosophila melanogaster	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for P04052 (Drosophila melanogaster) Explore P04052 Go to UniProtKB: P04052
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04052
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB2	M [auth B]	1,164	Drosophila melanogaster	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for P08266 (Drosophila melanogaster) Explore P08266 Go to UniProtKB: P08266
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08266
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB3	N [auth C]	269	Drosophila melanogaster	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for O97183 (Drosophila melanogaster) Explore O97183 Go to UniProtKB: O97183
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O97183
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC2	O [auth F]	84	Drosophila melanogaster	Mutation(s): 0
UniProt
Find proteins for Q24320 (Drosophila melanogaster) Explore Q24320 Go to UniProtKB: Q24320
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q24320
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC3	P [auth H]	147	Drosophila melanogaster	Mutation(s): 0
UniProt
Find proteins for Q9VNZ3 (Drosophila melanogaster) Explore Q9VNZ3 Go to UniProtKB: Q9VNZ3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9VNZ3
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB9	Q [auth I]	116	Drosophila melanogaster	Mutation(s): 0
UniProt
Find proteins for P36958 (Drosophila melanogaster) Explore P36958 Go to UniProtKB: P36958
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P36958
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC5	R [auth J]	67	Drosophila melanogaster	Mutation(s): 0
UniProt
Find proteins for Q9VC49 (Drosophila melanogaster) Explore Q9VC49 Go to UniProtKB: Q9VC49
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9VC49
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB11	S [auth K]	116	Drosophila melanogaster	Mutation(s): 0
UniProt
Find proteins for Q9VJE4 (Drosophila melanogaster) Explore Q9VJE4 Go to UniProtKB: Q9VJE4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9VJE4
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB12	T [auth L]	46	Drosophila melanogaster	Mutation(s): 0
UniProt
Find proteins for Q6IGE3 (Drosophila melanogaster) Explore Q6IGE3 Go to UniProtKB: Q6IGE3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6IGE3
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Reference Sequence

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB5	U [auth E]	210	Drosophila melanogaster	Mutation(s): 0
UniProt
Find proteins for Q7JZF5 (Drosophila melanogaster) Explore Q7JZF5 Go to UniProtKB: Q7JZF5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7JZF5
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Reference Sequence

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Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA	A [auth R]	10	Drosophila melanogaster
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
Template DNA	B [auth T]	174	Drosophila melanogaster
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Length	Organism	Image
Non-template DNA	C [auth N]	163	Drosophila melanogaster
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Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth I] SDF format, chain BA [auth J] SDF format, chain CA [auth L] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth B] SDF format, chain Z [auth I] SDF format, chain Y [auth C] MOL2 format, chain AA [auth I] MOL2 format, chain BA [auth J] MOL2 format, chain CA [auth L] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Z [auth I] MOL2 format, chain Y [auth C] mmCIF format, chain AA [auth I] mmCIF format, chain BA [auth J] mmCIF format, chain CA [auth L] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth B] mmCIF format, chain Z [auth I] mmCIF format, chain Y [auth C]	AA [auth I] BA [auth J] CA [auth L] V [auth A] W [auth A] AA [auth I], BA [auth J], CA [auth L], V [auth A], W [auth A], X [auth B], Y [auth C], Z [auth I]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth I] Focus chain BA [auth J] Focus chain CA [auth L] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth B] Focus chain Y [auth C] Focus chain Z [auth I] Interactions & Density Focus chain AA [auth I] Focus chain BA [auth J] Focus chain CA [auth L] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth B] Focus chain Y [auth C] Focus chain Z [auth I]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 7.80 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

Revision History (Full details and data files)

Version 1.0: 2025-02-19
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

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Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 9MU9 | pdb_00009mu9

Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Composite map

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

Entity ID: 4

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Sequence Annotations

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

9MU9 | pdb_00009mu9