9R2U | pdb_00009r2u

Drosophila MSL HAT nucleosome complex H4K16ac post-catalytic state

PDB DOI: https://doi.org/10.2210/pdb9R2U/pdb
EM Map EMD-53542: EMDB EMDataResource

Classification: NUCLEAR PROTEIN
Organism(s): Homo sapiens, synthetic construct, Drosophila melanogaster
Expression System: Escherichia coli, Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2025-05-01 Released: 2026-10-14
Deposition Author(s): Mueller, M., Kolesnikova, O., Doudin, M., Hoffmann, T., Becker, P., Eustermann, S.
Funding Organization(s): German Research Foundation (DFG), Boehringer Ingelheim Fonds (BIF)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 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

To Be Published

Mueller, M., Kolesnikova, O., Doudin, M., Thomae, A.W., Campos-Sparr, A., Kraus, S., Hoffmann, T., Becker, P., Eustermann, S.

To be published.

Macromolecule Content

Total Structure Weight: 519.81 kDa
Atom Count: 18,584
Modeled Residue Count: 1,837
Deposited Residue Count: 3,824
Unique protein chains: 8
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	A, E	135	Homo sapiens	Mutation(s): 0 Gene Names: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB... H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431 Go to UniProtKB: P68431
PHAROS: P68431 GTEx: ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68431
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Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B	102	Homo sapiens	Mutation(s): 0 Gene Names: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G... H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4C16, H4-16, HIST4H4
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805 Go to UniProtKB: P62805
PHAROS: P62805 GTEx: ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62805
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1-C	C, G	129	Homo sapiens	Mutation(s): 0 Gene Names: H2AC6, H2AFL, HIST1H2AC
UniProt & NIH Common Fund Data Resources
Find proteins for Q93077 (Homo sapiens) Explore Q93077 Go to UniProtKB: Q93077
PHAROS: Q93077 GTEx: ENSG00000180573
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q93077
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-C/E/F/G/I	D, H	125	Homo sapiens	Mutation(s): 0 Gene Names: HIST1H2BC, H2BFL, HIST1H2BE, H2BFH, HIST1H2BF, H2BFG, HIST1H2BG, H2BFA, HIST1H2BI, H2BFK
UniProt & NIH Common Fund Data Resources
Find proteins for P62807 (Homo sapiens) Explore P62807 Go to UniProtKB: P62807
PHAROS: P62807 GTEx: ENSG00000180596 ENSG00000277224 ENSG00000278588 ENSG00000273802 ENSG00000274290
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62807
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	F	102	Homo sapiens	Mutation(s): 0 Gene Names: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D... HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805 Go to UniProtKB: P62805
PHAROS: P62805 GTEx: ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62805
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Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein male-specific lethal-1	K [auth M]	1,047	Drosophila melanogaster	Mutation(s): 0 Gene Names: msl-1, CG10385
UniProt
Find proteins for P50535 (Drosophila melanogaster) Explore P50535 Go to UniProtKB: P50535
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P50535
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein male-specific lethal-3	L [auth N]	518	Drosophila melanogaster	Mutation(s): 2 Gene Names: msl-3, CG8631
UniProt
Find proteins for P50536 (Drosophila melanogaster) Explore P50536 Go to UniProtKB: P50536
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P50536
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone acetyltransferase MOF	M [auth O]	827	Drosophila melanogaster	Mutation(s): 0 Gene Names: mof, CG3025 EC: 2.3.1.48
UniProt
Find proteins for O02193 (Drosophila melanogaster) Explore O02193 Go to UniProtKB: O02193
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O02193
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 6
DNA	I	225	synthetic construct
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 7
DNA	J	225	synthetic construct
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Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA Query on COA Download:Ideal Coordinates CCD File SDF format, chain O MOL2 format, chain O mmCIF format, chain O	O	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain O Interactions & Density Focus chain O
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain N [auth O] MOL2 format, chain N [auth O] mmCIF format, chain N [auth O]	N [auth O]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain N [auth O] Interactions & Density Focus chain N [auth O]