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- EMDB-53543: Drosophila MSL HAT nucleosome complex H3K36me3 reader state -

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Basic information

Entry
Database: EMDB / ID: EMD-53543
TitleDrosophila MSL HAT nucleosome complex H3K36me3 reader state
Map dataMSL HAT nucleosome complex MSL3 H36me3 reader state
Sample
  • Complex: MSL HAT nucleosome complex
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-C
    • Protein or peptide: Histone H2B type 1-C/E/F/G/I
    • DNA: DNA
    • DNA: DNA
    • Protein or peptide: Protein male-specific lethal-3
KeywordsHistone Acetyltransferase Complex / NUCLEAR PROTEIN
Function / homology
Function and homology information


regulation of hemocyte proliferation / histone H4K20me1 reader activity / X chromosome located dosage compensation complex, transcription activating / oocyte development / MSL complex / dosage compensation by hyperactivation of X chromosome / histone H3K36me3 reader activity / chromocenter / HATs acetylate histones / histone H4K20me2 reader activity ...regulation of hemocyte proliferation / histone H4K20me1 reader activity / X chromosome located dosage compensation complex, transcription activating / oocyte development / MSL complex / dosage compensation by hyperactivation of X chromosome / histone H3K36me3 reader activity / chromocenter / HATs acetylate histones / histone H4K20me2 reader activity / germ cell development / X chromosome / nuclear chromosome / lncRNA binding / histone H4K16ac reader activity / 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 / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / Senescence-Associated Secretory Phenotype (SASP) / heterochromatin formation / Oxidative Stress Induced Senescence / antibacterial humoral response / Estrogen-dependent gene expression / chromosome, telomeric region / defense response to Gram-positive bacterium / Ub-specific processing proteases / cadherin binding / negative regulation of cell population proliferation
Similarity search - Function
: / MSL3 chromodomain-like / MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / Chromo-like domain superfamily / : / : ...: / MSL3 chromodomain-like / MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / Chromo-like domain superfamily / : / : / 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
Similarity search - Domain/homology
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 speciesDrosophila melanogaster (fruit fly) / Homo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsMueller M / Kolesnikova O / Doudin M / Hoffmann T / Becker P / Eustermann S
Funding support Germany, 3 items
OrganizationGrant numberCountry
German Research Foundation (DFG)Be1140/9-1 Germany
German Research Foundation (DFG)Be1140/11-1 Germany
Boehringer Ingelheim Fonds (BIF) Germany
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMay 1, 2025-
Header (metadata) releaseOct 14, 2026-
Map releaseOct 14, 2026-
UpdateOct 14, 2026-
Current statusOct 14, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53543.png

Downloads & links

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Map

FileDownload / File: emd_53543.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMSL HAT nucleosome complex MSL3 H36me3 reader state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 256 pix.
= 238.592 Å		0.93 Å/pix.
x 256 pix.
= 238.592 Å		0.93 Å/pix.
x 256 pix.
= 238.592 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0045
Minimum - Maximum-0.0135847395 - 0.028132075
Average (Standard dev.)0.00011066893 (±0.0011590029)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.592 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53543_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53543_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53543_half_map_2.map
Projections & Slices
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Sample components

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Entire : MSL HAT nucleosome complex

EntireName: MSL HAT nucleosome complex
Components
  • Complex: MSL HAT nucleosome complex
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-C
    • Protein or peptide: Histone H2B type 1-C/E/F/G/I
    • DNA: DNA
    • DNA: DNA
    • Protein or peptide: Protein male-specific lethal-3

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Supramolecule #1: MSL HAT nucleosome complex

SupramoleculeName: MSL HAT nucleosome complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Details: MSL HAT complex bound to H3K36me3 modified nucleosome
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Macromolecule #1: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.348051 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGV(M3L)KPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQ DFK TDLRFQSSAV MALQEACEAY LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3.1

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.30426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKGGKGL GKGGA(ALY)RHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHA KRK TVTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 1-C

MacromoleculeName: Histone H2A type 1-C / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.004329 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKQGGKA RAKAKSRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAIRN DEELNKLLGR VTIAQGGVLP NIQAVLLPKK TESHHKAKGK

UniProtKB: Histone H2A type 1-C

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Macromolecule #4: Histone H2B type 1-C/E/F/G/I

MacromoleculeName: Histone H2B type 1-C/E/F/G/I / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.806018 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PEPAKSAPAP KKGSKKAVTK AQKKDGKKRK RSRKESYSVY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSSK

UniProtKB: Histone H2B type 1-C/E/F/G/I

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Macromolecule #7: Protein male-specific lethal-3

MacromoleculeName: Protein male-specific lethal-3 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 59.756578 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHTEL RDETPLFHKG EIVLCYEPDK SKARVLYTSK VLNVFERRNE HGLRFYEYKI HFQGWRPSYD RCVRATVLLK DTEENRQLQ RELAEAAKLQ IRGDYSYKGT PDKPSAKKKR GGKAAHVEEP IVVPMDTGHL EAEHEMAPTP RAAGNRTRDN S GGKRKEKP ...String:
MHHHHHHTEL RDETPLFHKG EIVLCYEPDK SKARVLYTSK VLNVFERRNE HGLRFYEYKI HFQGWRPSYD RCVRATVLLK DTEENRQLQ RELAEAAKLQ IRGDYSYKGT PDKPSAKKKR GGKAAHVEEP IVVPMDTGHL EAEHEMAPTP RAAGNRTRDN S GGKRKEKP PSGDGRLKGN RGRQTETFYN NTINDVSVYN HVPQEDRIMM RVSERLRELI EYDRNMIKVL GKQHALPARV PI VTIMENF VKQQAVELAI SIKQDSSRAR NTQSRNARME REYDRVMSTV CMLKEVVDGL RIYFEFHVDD HLLYTEEKEY VHN YLTDDN MRNCSLILNK SYEYINPSGD TELIGLDGTP VGEGSGDTNG QIGVINIGGP EYEKQLQKCL LYIVTASGKN TAQA YERTS PYTAAYKLPV EMRGFLNETF KWRLLSAESP PEKSMVFGAP HLVRLMIKMP MFLNASPISN KKLEDLLPHL DAFIN YLEN HREWFDRENF VNSTALPQED LQRELLDSLD GIAA

UniProtKB: Protein male-specific lethal-3

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Macromolecule #5: DNA

MacromoleculeName: DNA / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 69.264109 KDa
SequenceString: (DG)(DG)(DA)(DC)(DC)(DC)(DT)(DA)(DT)(DA) (DC)(DG)(DC)(DG)(DG)(DC)(DC)(DG)(DC)(DC) (DA)(DA)(DG)(DA)(DA)(DC)(DA)(DC)(DG) (DG)(DT)(DT)(DT)(DA)(DG)(DA)(DA)(DA)(DG) (DA) (DG)(DA)(DT)(DA)(DG)(DT) ...String:
(DG)(DG)(DA)(DC)(DC)(DC)(DT)(DA)(DT)(DA) (DC)(DG)(DC)(DG)(DG)(DC)(DC)(DG)(DC)(DC) (DA)(DA)(DG)(DA)(DA)(DC)(DA)(DC)(DG) (DG)(DT)(DT)(DT)(DA)(DG)(DA)(DA)(DA)(DG) (DA) (DG)(DA)(DT)(DA)(DG)(DT)(DA)(DT) (DT)(DA)(DC)(DA)(DC)(DC)(DT)(DG)(DG)(DA) (DG)(DA) (DA)(DT)(DC)(DC)(DC)(DG)(DG) (DT)(DG)(DC)(DC)(DG)(DA)(DG)(DG)(DC)(DC) (DG)(DC)(DT) (DC)(DA)(DA)(DT)(DT)(DG) (DG)(DT)(DC)(DG)(DT)(DA)(DG)(DC)(DA)(DA) (DG)(DC)(DT)(DC) (DT)(DA)(DG)(DC)(DA) (DC)(DC)(DG)(DC)(DT)(DT)(DA)(DA)(DA)(DC) (DG)(DC)(DA)(DC)(DG) (DT)(DA)(DC)(DG) (DC)(DG)(DC)(DT)(DG)(DT)(DC)(DC)(DC)(DC) (DC)(DG)(DC)(DG)(DT)(DT) (DT)(DT)(DA) (DA)(DC)(DC)(DG)(DC)(DC)(DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT)(DT)(DA)(DC) (DT)(DC) (DC)(DC)(DT)(DA)(DG)(DT)(DC)(DT)(DC)(DC) (DA)(DG)(DG)(DC)(DA)(DC)(DG)(DT) (DG) (DT)(DC)(DA)(DG)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DC)(DA)(DT)(DC)(DC)(DT)(DG)(DT) (DG)(DC)(DA)(DT)(DG)(DT)(DA)(DT)(DT)(DG) (DA)(DA)(DC)(DA)(DG)(DC)(DG)(DA)(DC)(DC) (DT)(DT)(DG)(DC)(DC)

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Macromolecule #6: DNA

MacromoleculeName: DNA / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 69.681328 KDa
SequenceString: (DG)(DG)(DC)(DA)(DA)(DG)(DG)(DT)(DC)(DG) (DC)(DT)(DG)(DT)(DT)(DC)(DA)(DA)(DT)(DA) (DC)(DA)(DT)(DG)(DC)(DA)(DC)(DA)(DG) (DG)(DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA) (DT) (DC)(DT)(DG)(DA)(DC)(DA) ...String:
(DG)(DG)(DC)(DA)(DA)(DG)(DG)(DT)(DC)(DG) (DC)(DT)(DG)(DT)(DT)(DC)(DA)(DA)(DT)(DA) (DC)(DA)(DT)(DG)(DC)(DA)(DC)(DA)(DG) (DG)(DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA) (DT) (DC)(DT)(DG)(DA)(DC)(DA)(DC)(DG) (DT)(DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA) (DC)(DT) (DA)(DG)(DG)(DG)(DA)(DG)(DT) (DA)(DA)(DT)(DC)(DC)(DC)(DC)(DT)(DT)(DG) (DG)(DC)(DG) (DG)(DT)(DT)(DA)(DA)(DA) (DA)(DC)(DG)(DC)(DG)(DG)(DG)(DG)(DG)(DA) (DC)(DA)(DG)(DC) (DG)(DC)(DG)(DT)(DA) (DC)(DG)(DT)(DG)(DC)(DG)(DT)(DT)(DT)(DA) (DA)(DG)(DC)(DG)(DG) (DT)(DG)(DC)(DT) (DA)(DG)(DA)(DG)(DC)(DT)(DT)(DG)(DC)(DT) (DA)(DC)(DG)(DA)(DC)(DC) (DA)(DA)(DT) (DT)(DG)(DA)(DG)(DC)(DG)(DG)(DC)(DC)(DT) (DC)(DG)(DG)(DC)(DA)(DC)(DC) (DG)(DG) (DG)(DA)(DT)(DT)(DC)(DT)(DC)(DC)(DA)(DG) (DG)(DT)(DG)(DT)(DA)(DA)(DT)(DA) (DC) (DT)(DA)(DT)(DC)(DT)(DC)(DT)(DT)(DT)(DC) (DT)(DA)(DA)(DA)(DC)(DC)(DG)(DT)(DG) (DT)(DT)(DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG) (DC)(DC)(DG)(DC)(DG)(DT)(DA)(DT)(DA)(DG) (DG)(DG)(DT)(DC)(DC)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.47 mg/mL
BufferpH: 7.5
Details: 0.5 mM Acetyl CoA, 0.05% beta octyl glucosise, 3 mM Hepes pH7.5, 7.5 mM KCl, 1.5 uM ZnCl2, 0.075 mM DTT, 17.5 mM TrisHCl, pH 7.5 35 mM NaCl
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV
DetailsFor CryoEM vitrication, the MSL-HAT core complex and H3K36me3 modified mononucleosomes were incubated in a 1:1 ratio with 0.5 mM Acetyl-CoA for 5-10 min on ice

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: SerialEM
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 55.72 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 914355
Details: WARP pretrained BoxNet2Mask_20180918 model, TOPAZ trained model, RELION 3D reference based picking
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 33389
Initial angle assignmentType: OTHER / Details: cryoSPARC ab initio model generation
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: OTHER
Output model

PDB-9r2w:
Drosophila MSL HAT nucleosome complex H3K36me3 reader state

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