EMDB-53542: Drosophila MSL HAT nucleosome complex H4K16ac post-catalytic state

Basic information

Entry

Database: EMDB / ID: EMD-53542

• Title: Drosophila MSL HAT nucleosome complex H4K16ac post-catalytic state
• Map data: Drosophila MSL nucleosome H4K16ac post-catalytic state

Sample

• Complex: MSL HAT nucleosome complex
  • Protein or peptide: x 8 types
  • DNA: x 2 types
• Ligand: x 2 types

• Keywords: Histone Acetyltransferase Complex / NUCLEAR PROTEIN

Function / homology

Function:

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

Domain/homology:

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

Component:

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

• Biological species: Drosophila melanogaster (fruit fly) / Homo sapiens (human) / synthetic construct (others)
• Method: single particle reconstruction / cryo EM / Resolution: 3.2 Å
• Authors: Mueller M / Kolesnikova O / Doudin M / Hoffmann T / Becker P / Eustermann S

Funding support

Germany, 3 items

Organization	Grant number	Country
German Research Foundation (DFG)	Be1140/9-1	Germany
German Research Foundation (DFG)	Be1140/11-1	Germany
Boehringer Ingelheim Fonds (BIF)		Germany

• Citation: Journal: To Be Published; Title: To Be Published; Authors: Mueller M / Kolesnikova O / Doudin M / Thomae AW / Campos-Sparr A / Kraus S / Hoffmann T / Becker P / Eustermann S

History

Deposition	May 1, 2025	-
Header (metadata) release	Oct 14, 2026	-
Map release	Oct 14, 2026	-
Update	Oct 14, 2026	-
Current status	Oct 14, 2026	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_53542.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: Drosophila MSL nucleosome H4K16ac post-catalytic state
• Voxel size: X=Y=Z: 0.93 Å

Density

Contour Level	By AUTHOR: 0.83
Minimum - Maximum	-5.3563 - 8.299246999999999
Average (Standard dev.)	-0.001515294 (±0.23661412)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order Z Y X Origin 0 0 0 Dimensions 256 256 256 Spacing 256 256 256
Cell	A=B=C: 238.08 Å α=β=γ: 90.0 °

Supplemental data

Sample components

Entire : MSL HAT nucleosome complex

• Entire: Name: 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
  • Protein or peptide: Histone H4
  • DNA: DNA
  • DNA: DNA
  • Protein or peptide: Protein male-specific lethal-1
  • Protein or peptide: Protein male-specific lethal-3
  • Protein or peptide: Histone acetyltransferase MOF
• Ligand: ZINC ION
• Ligand: COENZYME A

Supramolecule #1: MSL HAT nucleosome complex

• Supramolecule: Name: MSL HAT nucleosome complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10; Details: catalytically active MSL HAT complex bound to nucleosome, post-catalytic state of H4 K16Ac modification
• Source (natural): Organism: Drosophila melanogaster (fruit fly)

Macromolecule #1: Histone H3.1

• Macromolecule: Name: Histone H3.1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 15.305969 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEACEAY LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3.1

Macromolecule #2: Histone H4

• Macromolecule: Name: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 11.30426 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

SGRGKGGKGL GKGGA(ALY)RHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHA KRK TVTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

Macromolecule #3: Histone H2A type 1-C

• Macromolecule: Name: Histone H2A type 1-C / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 14.004329 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

SGRGKQGGKA RAKAKSRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAIRN DEELNKLLGR VTIAQGGVLP NIQAVLLPKK TESHHKAKGK

UniProtKB: Histone H2A type 1-C

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

• Macromolecule: Name: 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 weight: Theoretical: 13.806018 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

PEPAKSAPAP KKGSKKAVTK AQKKDGKKRK RSRKESYSVY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSSK

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

Macromolecule #5: Histone H4

• Macromolecule: Name: Histone H4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 11.263231 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

Macromolecule #8: Protein male-specific lethal-1

• Macromolecule: Name: Protein male-specific lethal-1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Drosophila melanogaster (fruit fly)
• Molecular weight: Theoretical: 118.681414 KDa
• Recombinant expression: Organism: Spodoptera frugiperda (fall armyworm)

Sequence

String:

MDKRFKWPPK KRANYLESPY PHIPSRGRQR NLHGHPNQTQ HLHQHPGKIY ERQQYGNGRG GHGGGNNNYR KLLHSLPAEH GGGAMAPPS SGGTVCAGAD MVKLISENNN LRRMVMLNLN LMQEQTDSIA AKDKELDDQS AKMSVVKAQN EELKQAVAQL E AANQELCK QLRRKNQRRN DNDDDDDDPP LPPAAPQQKL IRCHAETQTV FREREQGTQT IDAQPQFANA LPRGINMKES PA LDHHAGA VTNQPASKRS ESKGRGEFNG KKVSTFILQR MNQDFEHHIH EQTEVAEEHE MEAHKEQISQ EEDQLVAEED HLH MQEVHT EEVVGGDIFH DALESIEMEV VTEELVDMEE HGQSVDANGH IEEDDDEDDE DDENSDKDDD SEEDDYPWMH SDAD VNART EEELWQNQNY LLELDPTEEK TCAPSAHSTP NHQQKSSTQA EIRKEGNQNR ITEKLLQLKP EPMVDALEAP ILPKW VAFK KKDKEHESVP ESPEVPKQQP HQEDAIVDHN AIKNQLEVPK PDLKPKDQPK DEQRQDGQLD VRVEPQEDVR KVQKET LKR QPEDAPKHLP KAVAPKVTKT SSRESTLPKA NTADIKDAPA QKVIANHQST KTQTDPVKTQ RLQVKIRQYE MHPDMRT GS SAPSDIRKQK NVDPVSTPET KTIKSKSMLV NDKKTTSETS QSPDQEIDVE TVRRKLAEHL KKELLSQSHS SQVTLKKI R ERVATNLIYP PPSAPVSSTT ITPAPTPSTT PTPGSTPQHA VTSSMDQEIS AAKSKSKAAE QIATPLTPQS NSSVSSTTS TIRKTLNNCS PHTYSKATAR SGKLQSRFRT ATFPYSTRTW EDQEFHCDNE FFLEEADELL ADNPSLEIPK WRDVPVPPSS DKIDTELLS DATFERRHQK YVKDEVDRKC RDARYMKEQI RLEQLRMRRN QDEVLVALDP LRASTFYPLP EDIEAIQFVN E VTVQAFGE NVVNMEARDD FGVPWVDAIE APTSIARSKA LAEPVATLAS KKIPTTAAEA RHQENHSSYV FPKRRKRQKN RD YKDDDDK

UniProtKB: Protein male-specific lethal-1

Macromolecule #9: Protein male-specific lethal-3

• Macromolecule: Name: Protein male-specific lethal-3 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Drosophila melanogaster (fruit fly)
• Molecular weight: Theoretical: 59.756578 KDa
• Recombinant expression: Organism: Spodoptera frugiperda (fall armyworm)

Sequence

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

Macromolecule #10: Histone acetyltransferase MOF

• Macromolecule: Name: Histone acetyltransferase MOF / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO / EC number: histone acetyltransferase
• Source (natural): Organism: Drosophila melanogaster (fruit fly)
• Molecular weight: Theoretical: 92.797602 KDa
• Recombinant expression: Organism: Spodoptera frugiperda (fall armyworm)

Sequence

String:

MSEAELEQTP SAGHVQEQPI EEEHEPEQEP TDAYTIGGPP RTPVEDAAAE LSASLDVSGS DQSAEQSLDL SGVQAEAAAE SEPPAKRQH RDISPISEDS TPASSTSTSS TRSSSSSRYD DVSEAEEAPP EPEPEQPQQQ QQEEKKEDGQ DQVKSPGPVE L EAQEPAQP QKQKEVVDQE IETEDEPSSD TVICVADINP YGSGSNIDDF VMDPDAPPNA IITEVVTIPA PLHLKGTQQL GL PLAAPPP PPPPPAAEQV PETPASPTDD GEEPPAVYLS PYIRSRYMQE STPGLPTRLA PRDPRQRNMP PPAVVLPIQT VLS ANVEAI SDDSSETSSS DDDEEEEEDE DDALTMEHDN TSRETVITTG DPLMQKIDIS ENPDKIYFIR REDGTVHRGQ VLQS RTTEN AAAPDEYYVH YVGLNRRLDG WVGRHRISDN ADDLGGITVL PAPPLAPDQP STSREMLAQQ AAAAAAASSE RQKRA ANKD YYLSYCENSR YDYSDRKMTR YQKRRYDEIN HVQKSHAELT ATQAALEKEH ESITKIKYID KLQFGNYEID TWYFSP FPE EYGKARTLYV CEYCLKYMRF RSSYAYHLHE CDRRRPPGRE IYRKGNISIY EVNGKEESLY CQLLCLMAKL FLDH (ALY)VLYF DMDPFLFYIL CETDKEGSHI VGYFSKEKKS LENYNVACIL VLPPHQRKGF GKLLIAFSYE LSRKEGVIGS P EKPLSDLG RLSYRSYWAY TLLELMKTRC APEQITIKEL SEMSGITHDD IIYTLQSMKM IKYWKGQNVI CVTSKTIQDH LQ LPQFKQP KLTIDTDYLV WSPQTAAAVV RAPGNSG

UniProtKB: Histone acetyltransferase MOF

Macromolecule #6: DNA

• Macromolecule: Name: DNA / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: synthetic construct (others)
• Molecular weight: Theoretical: 69.264109 KDa

Sequence

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)

Macromolecule #7: DNA

• Macromolecule: Name: DNA / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: synthetic construct (others)
• Molecular weight: Theoretical: 69.681328 KDa

Sequence

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)

Macromolecule #11: ZINC ION

• Macromolecule: Name: ZINC ION / type: ligand / ID: 11 / Number of copies: 1 / Formula: ZN
• Molecular weight: Theoretical: 65.409 Da

Macromolecule #12: COENZYME A

• Macromolecule: Name: COENZYME A / type: ligand / ID: 12 / Number of copies: 1 / Formula: COA
• Molecular weight: Theoretical: 767.534 Da

Chemical component information

ChemComp-COA:
COENZYME A

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Concentration: 0.516 mg/mL
• Buffer: pH: 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
• Grid: Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: OTHER
• Vitrification: Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV
• 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

Electron microscopy

• Microscope: TFS KRIOS
• Software: Name: SerialEM
• Image recording: Film or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 48.97 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 130000
• Sample stage: Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Particle selection: Number selected: 1152900 ; Details: WARP pretrained BoxNet2Mask_20180918 model, TOPAZ trained model, RELION 3D reference based picking
• CTF correction: Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
• Startup model: Type of model: NONE
• Final reconstruction: Applied symmetry - Point group: C₁ (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 92666
• Initial angle assignment: Type: OTHER / Details: cryoSPARC ab initio model generation
• Final angle assignment: Type: MAXIMUM LIKELIHOOD

Atomic model buiding 1

• Refinement: Protocol: OTHER

Output model

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