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- PDB-9r2u: Drosophila MSL HAT nucleosome complex H4K16ac post-catalytic state -

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Entry
Database: PDB / ID: 9r2u
TitleDrosophila MSL HAT nucleosome complex H4K16ac post-catalytic state
Components
  • (DNA) x 2
  • (Histone H4) x 2
  • (Protein male-specific lethal- ...) x 2
  • Histone H2A type 1-C
  • Histone H2B type 1-C/E/F/G/I
  • Histone H3.1
  • Histone acetyltransferase MOF
KeywordsNUCLEAR PROTEIN / Histone Acetyltransferase Complex
Function / homology
Function and homology information


dosage compensation complex / regulation of hemocyte proliferation / polytene chromosome interband / Formation of WDR5-containing histone-modifying complexes / histone H4K20me1 reader activity / positive regulation of gene expression, epigenetic / X chromosome located dosage compensation complex, transcription activating / oocyte development / MSL complex / histone H4K16 acetyltransferase activity ...dosage compensation complex / regulation of hemocyte proliferation / polytene chromosome interband / Formation of WDR5-containing histone-modifying complexes / histone H4K20me1 reader activity / positive regulation of gene expression, epigenetic / X chromosome located dosage compensation complex, transcription activating / oocyte development / MSL complex / histone H4K16 acetyltransferase activity / dosage compensation by hyperactivation of X chromosome / histone H3K36me3 reader activity / chromocenter / HATs acetylate histones / histone H4K20me2 reader activity / germ cell development / NSL complex / X chromosome / histone acetyltransferase activity / NuA4 histone acetyltransferase complex / nuclear chromosome / lncRNA binding / histone H4K16ac reader activity / DNA repair-dependent chromatin remodeling / histone acetyltransferase / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / histone reader activity / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / telomere organization / Interleukin-7 signaling / ChAHP complex assembly / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / FXIIa activates plasma kallikrein-kinin system / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / Meiotic synapsis / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / DNA damage response, signal transduction by p53 class mediator / PRC2 methylates histones and DNA / NuRD complex assembly / Regulation of endogenous retroelements by KRAB-ZFP proteins / Interaction of NuRD complexes with transcription factors / Defective pyroptosis / HDACs deacetylate histones / CHD1 and CHD2 subfamily / Transcriptional regulation by small RNAs / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / epigenetic regulation of gene expression / CHD6, CHD7, CHD8, CHD9 subfamily / HDMs demethylate histones / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Negative Regulation of CDH1 Gene Transcription / NoRC negatively regulates rRNA expression / PKMTs methylate histone lysines / G2/M DNA damage checkpoint / Formation of the beta-catenin:TCF transactivating complex / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / RMTs methylate histone arginines / HCMV Early Events / Metalloprotease DUBs / nucleosomal DNA binding / innate immune response in mucosa / structural constituent of chromatin / nucleosome assembly / Regulation of PD-L1(CD274) transcription / UCH proteinases / nucleosome / HATs acetylate histones / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Processing of DNA double-strand break ends / Dengue Virus-Host Interactions
Similarity search - Function
Protein male-specific lethal-1 / PEHE domain / PEHE domain profile. / PEHE domain / PEHE / : / MSL3 chromodomain-like / MRG / MRG domain / MRG, C-terminal domain superfamily ...Protein male-specific lethal-1 / PEHE domain / PEHE domain profile. / PEHE domain / PEHE / : / MSL3 chromodomain-like / MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / : / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / RNA binding activity-knot of a chromodomain / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / RNA binding activity-knot of a chromodomain / Chromo-like domain superfamily / Acyl-CoA N-acyltransferase / : / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
COENZYME A / DNA / DNA (> 10) / DNA (> 100) / Histone acetyltransferase MOF / Protein male-specific lethal-1 / Protein male-specific lethal-3 / Histone H4 / Histone H2B type 1-C/E/F/G/I / Histone H3.1 / Histone H2A type 1-C
Similarity search - Component
Biological speciesHomo sapiens (human)
Drosophila melanogaster (fruit fly)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsMueller, M. / Kolesnikova, O. / Doudin, M. / Hoffmann, T. / Becker, P. / Eustermann, S.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)Be1140/9-1 Germany
German Research Foundation (DFG)Be1140/11-1 Germany
Boehringer Ingelheim Fonds (BIF) Germany
CitationJournal: To Be Published
Title: To Be Published
Authors: Mueller, M. / Kolesnikova, O. / Doudin, M. / Thomae, A.W. / Campos-Sparr, A. / Kraus, S. / Hoffmann, T. / Becker, P. / Eustermann, S.
History
DepositionMay 1, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 14, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone H3.1
B: Histone H4
C: Histone H2A type 1-C
D: Histone H2B type 1-C/E/F/G/I
E: Histone H3.1
F: Histone H4
G: Histone H2A type 1-C
H: Histone H2B type 1-C/E/F/G/I
I: DNA
J: DNA
M: Protein male-specific lethal-1
N: Protein male-specific lethal-3
O: Histone acetyltransferase MOF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)519,81415
Polymers518,98113
Non-polymers8332
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 6 types, 9 molecules AEBCGDHFO

#1: Protein Histone H3.1 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 15305.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: 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, ...Gene: 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
Production host: Escherichia coli (E. coli) / References: UniProt: P68431
#2: Protein Histone H4


Mass: 11304.260 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: 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, ...Gene: 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
Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#3: Protein Histone H2A type 1-C / H2A-clustered histone 6 / Histone H2A/l


Mass: 14004.329 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2AC6, H2AFL, HIST1H2AC / Production host: Escherichia coli (E. coli) / References: UniProt: Q93077
#4: Protein Histone H2B type 1-C/E/F/G/I / Histone H2B.1 A / Histone H2B.a / H2B/a / Histone H2B.g / H2B/g / Histone H2B.h / H2B/h / Histone ...Histone H2B.1 A / Histone H2B.a / H2B/a / Histone H2B.g / H2B/g / Histone H2B.h / H2B/h / Histone H2B.k / H2B/k / Histone H2B.l / H2B/l


Mass: 13806.018 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H2BC, H2BFL, HIST1H2BE, H2BFH, HIST1H2BF, H2BFG, HIST1H2BG, H2BFA, HIST1H2BI, H2BFK
Production host: Escherichia coli (E. coli) / References: UniProt: P62807
#5: Protein Histone H4


Mass: 11263.231 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: 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, ...Gene: 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
Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#10: Protein Histone acetyltransferase MOF / Males-absent on the first protein


Mass: 92797.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: mof, CG3025 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O02193, histone acetyltransferase

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DNA chain , 2 types, 2 molecules IJ

#6: DNA chain DNA


Mass: 69264.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain DNA


Mass: 69681.328 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein male-specific lethal- ... , 2 types, 2 molecules MN

#8: Protein Protein male-specific lethal-1


Mass: 118681.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: msl-1, CG10385 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P50535
#9: Protein Protein male-specific lethal-3


Mass: 59756.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: msl-3, CG8631 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P50536

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Non-polymers , 2 types, 2 molecules

#11: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#12: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: MSL HAT nucleosome complex / Type: COMPLEX
Details: catalytically active MSL HAT complex bound to nucleosome, post-catalytic state of H4 K16Ac modification
Entity ID: #1-#10 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
Details: 0.5 mM Acetyl CoA, 2 mM Hepes pH 7.5, 42 mM KCl,17,5 mM Tris HCl pH7.5,35 mM NaCl,0.05% (w/V) beta octyl-glucoside
SpecimenConc.: 0.516 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: For CryoEM vitrication, the MSL-HAT core complex and mononucleosomes were incubated in a 1:1 ratio with 0.5 mM Acetyl-CoA for 5-10 min on ice
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 600 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 48.97 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1Warpparticle selection
2PHENIX1.21.1_5286model refinement
3SerialEMimage acquisition
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1152900
Details: WARP pretrained BoxNet2Mask_20180918 model, TOPAZ trained model, RELION 3D reference based picking
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92666 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 25.83 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.012412798
ELECTRON MICROSCOPYf_angle_d0.971917240
ELECTRON MICROSCOPYf_chiral_restr0.06953077
ELECTRON MICROSCOPYf_plane_restr0.01062500
ELECTRON MICROSCOPYf_dihedral_angle_d25.86418132

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