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- EMDB-32150: NuA4 bound to the nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-32150
TitleNuA4 bound to the nucleosome
Map data
Sample
  • Complex: NuA4 bound to the nucleosome
    • Protein or peptide: x 14 types
    • DNA: x 2 types
  • Ligand: x 3 types
Function / homology
Function and homology information


PI5P Regulates TP53 Acetylation / NuA3b histone acetyltransferase complex / mitotic actomyosin contractile ring contraction / NuA3 histone acetyltransferase complex / NuA3a histone acetyltransferase complex / RHOA GTPase cycle / DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / cellular bud neck contractile ring / piccolo histone acetyltransferase complex ...PI5P Regulates TP53 Acetylation / NuA3b histone acetyltransferase complex / mitotic actomyosin contractile ring contraction / NuA3 histone acetyltransferase complex / NuA3a histone acetyltransferase complex / RHOA GTPase cycle / DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / cellular bud neck contractile ring / piccolo histone acetyltransferase complex / RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / ascospore wall assembly / vacuole inheritance / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / histone H4K16 acetyltransferase activity / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / SUMOylation of transcription cofactors / actin cortical patch / DNA-templated transcription elongation / positive regulation of triglyceride biosynthetic process / Swr1 complex / Platelet degranulation / histone H4 acetyltransferase activity / : / SLIK (SAGA-like) complex / rDNA heterochromatin formation / Ino80 complex / kinetochore assembly / peptide N-acetyltransferase activity / SWI/SNF complex / SAGA complex / NuA4 histone acetyltransferase complex / peptide-lysine-N-acetyltransferase activity / establishment of cell polarity / Estrogen-dependent gene expression / actin filament bundle / positive regulation of macroautophagy / protein secretion / chromosome organization / histone acetyltransferase activity / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / methylated histone binding / meiotic cell cycle / actin filament / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / endocytosis / structural constituent of chromatin / transcription corepressor activity / nucleosome / chromatin organization / histone binding / protein-containing complex assembly / regulation of cell cycle / hydrolase activity / chromatin remodeling / cell cycle / protein heterodimerization activity / DNA repair / negative regulation of DNA-templated transcription / DNA-templated transcription / chromatin binding / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol
Similarity search - Function
Chromatin modification-related protein Eaf6 / Histone acetyltransferase subunit NuA4 / SWR1-complex protein 4/DNA methyltransferase 1-associated protein 1 / DAMP1, SANT/Myb-like domain / SANT/Myb-like domain of DAMP1 / Enhancer of polycomb protein / Tra1, HEAT repeat ring region / Tra1, HEAT repeat central region / Tra1 HEAT repeat central region / Tra1 HEAT repeat ring region ...Chromatin modification-related protein Eaf6 / Histone acetyltransferase subunit NuA4 / SWR1-complex protein 4/DNA methyltransferase 1-associated protein 1 / DAMP1, SANT/Myb-like domain / SANT/Myb-like domain of DAMP1 / Enhancer of polycomb protein / Tra1, HEAT repeat ring region / Tra1, HEAT repeat central region / Tra1 HEAT repeat central region / Tra1 HEAT repeat ring region / Inhibitor of growth protein, N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / ING family / Myb-like domain profile. / domain in helicases and associated with SANT domains / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / Myb-like DNA-binding domain / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / PIK-related kinase, FAT / FAT domain / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / Zinc finger, PHD-type, conserved site / PHD-finger / Acyl-CoA N-acyltransferase / Zinc finger PHD-type signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Histone H3 signature 1. / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Homeobox-like domain superfamily / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / ATPase, nucleotide binding domain / Zinc finger, FYVE/PHD-type / Histone-fold / Armadillo-type fold / Zinc finger, RING/FYVE/PHD-type / Winged helix-like DNA-binding domain superfamily / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Histone H3 / Histone H2B 1.1 / Chromatin modification-related protein YNG2 / Transcription-associated protein 1 / Enhancer of polycomb-like protein 1 / Chromatin modification-related protein EAF6 / SWR1-complex protein 4 / Actin / Actin-related protein 4 / Chromatin modification-related protein EAF1 ...Histone H3 / Histone H2B 1.1 / Chromatin modification-related protein YNG2 / Transcription-associated protein 1 / Enhancer of polycomb-like protein 1 / Chromatin modification-related protein EAF6 / SWR1-complex protein 4 / Actin / Actin-related protein 4 / Chromatin modification-related protein EAF1 / Histone acetyltransferase ESA1 / Histone H2A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae S288C (yeast) / Xenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.8 Å
AuthorsQu K / Chen Z
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2022
Title: Structure of the NuA4 acetyltransferase complex bound to the nucleosome.
Authors: Keke Qu / Kangjing Chen / Hao Wang / Xueming Li / Zhucheng Chen /
Abstract: Deoxyribonucleic acid in eukaryotes wraps around the histone octamer to form nucleosomes, the fundamental unit of chromatin. The N termini of histone H4 interact with nearby nucleosomes and play an ...Deoxyribonucleic acid in eukaryotes wraps around the histone octamer to form nucleosomes, the fundamental unit of chromatin. The N termini of histone H4 interact with nearby nucleosomes and play an important role in the formation of high-order chromatin structure and heterochromatin silencing. NuA4 in yeast and its homologue Tip60 complex in mammalian cells are the key enzymes that catalyse H4 acetylation, which in turn regulates chromatin packaging and function in transcription activation and DNA repair. Here we report the cryo-electron microscopy structure of NuA4 from Saccharomyces cerevisiae bound to the nucleosome. NuA4 comprises two major modules: the catalytic histone acetyltransferase (HAT) module and the transcription activator-binding (TRA) module. The nucleosome is mainly bound by the HAT module and is positioned close to a polybasic surface of the TRA module, which is important for the optimal activity of NuA4. The nucleosomal linker DNA carrying the upstream activation sequence is oriented towards the conserved, transcription activator-binding surface of the Tra1 subunit, which suggests a potential mechanism of NuA4 to act as a transcription co-activator. The HAT module recognizes the disk face of the nucleosome through the H2A-H2B acidic patch and nucleosomal DNA, projecting the catalytic pocket of Esa1 to the N-terminal tail of H4 and supporting its function in selective acetylation of H4. Together, our findings illustrate how NuA4 is assembled and provide mechanistic insights into nucleosome recognition and transcription co-activation by a HAT.
History
DepositionNov 9, 2021-
Header (metadata) releaseAug 10, 2022-
Map releaseAug 10, 2022-
UpdateNov 16, 2022-
Current statusNov 16, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32150.png

Downloads & links

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Map

FileDownload / File: emd_32150.map.gz / Format: CCP4 / Size: 3.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 4.33 Å
Density
Contour LevelBy AUTHOR: 0.032
Minimum - Maximum-0.07677387 - 0.26781687
Average (Standard dev.)0.0006990877 (±0.014608934)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions949494
Spacing949494
CellA=B=C: 407.02 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : NuA4 bound to the nucleosome

EntireName: NuA4 bound to the nucleosome
Components
  • Complex: NuA4 bound to the nucleosome
    • Protein or peptide: Chromatin modification-related protein EAF6
    • Protein or peptide: Chromatin modification-related protein YNG2
    • Protein or peptide: Enhancer of polycomb-like protein 1
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B 1.1
    • Protein or peptide: Histone acetyltransferase ESA1
    • DNA: DNA (207-mer)
    • DNA: DNA (207-mer)
    • Protein or peptide: Epl1 arginine anchor
    • Protein or peptide: Chromatin modification-related protein EAF1
    • Protein or peptide: Actin-related protein 4
    • Protein or peptide: Actin
    • Protein or peptide: SWR1-complex protein 4
    • Protein or peptide: Transcription-associated protein 1
  • Ligand: CARBOXYMETHYL COENZYME *A
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: NuA4 bound to the nucleosome

SupramoleculeName: NuA4 bound to the nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Chromatin modification-related protein EAF6

MacromoleculeName: Chromatin modification-related protein EAF6 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 12.915704 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MTDELKSYEA LKAELKKSLQ DRREQEDTFD NLQQEIYDKE TEYFSHNSNN NHSGHGGAHG SKSHYSGNII KGFDTFSKSH HSHADSAFN NNDRIFSLSS ATYVKQQHGQ SQND

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Macromolecule #2: Chromatin modification-related protein YNG2

MacromoleculeName: Chromatin modification-related protein YNG2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 32.139514 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MDPSLVLEQT IQDVSNLPSE FRYLLEEIGS NDLKLIEEKK KYEQKESQIH KFIRQQGSIP KHPQEDGLDK EIKESLLKCQ SLQREKCVL ANTALFLIAR HLNKLEKNIA LLEEDGVLAP VEEDGDMDSA AEASRESSVV SNSSVKKRRA ASSSGSVPPT L KKKKTSRT ...String:
MDPSLVLEQT IQDVSNLPSE FRYLLEEIGS NDLKLIEEKK KYEQKESQIH KFIRQQGSIP KHPQEDGLDK EIKESLLKCQ SLQREKCVL ANTALFLIAR HLNKLEKNIA LLEEDGVLAP VEEDGDMDSA AEASRESSVV SNSSVKKRRA ASSSGSVPPT L KKKKTSRT SKLQNEIDVS SREKSVTPVS PSIEKKIART KEFKNSRNGK GQNGSPENEE EDKTLYCFCQ RVSFGEMVAC DG PNCKYEW FHYDCVNLKE PPKGTWYCPE CKIEMEKNKL KRKRN

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Macromolecule #3: Enhancer of polycomb-like protein 1

MacromoleculeName: Enhancer of polycomb-like protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 96.889867 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MPTPSNAIEI NDGSHKSGRS TRRSGSRSAH DDGLDSFSKG DSGAGASAGS SNSRFRHRKI SVKQHLKIYL PNDLKHLDKD ELQQREVVE IETGVEKNEE KEVHLHRILQ MGSGHTKHKD YIPTPDASMT WNEYDKFYTG SFQETTSYIK FSATVEDCCG T NYNMDERD ...String:
MPTPSNAIEI NDGSHKSGRS TRRSGSRSAH DDGLDSFSKG DSGAGASAGS SNSRFRHRKI SVKQHLKIYL PNDLKHLDKD ELQQREVVE IETGVEKNEE KEVHLHRILQ MGSGHTKHKD YIPTPDASMT WNEYDKFYTG SFQETTSYIK FSATVEDCCG T NYNMDERD ETFLNEQVNK GSSDILTEDE FEILCSSFEH AIHERQPFLS MDPESILSFE ELKPTLIKSD MADFNLRNQL NH EINSHKT HFITQFDPVS QMNTRPLIQL IEKFGSKIYD YWRERKIEVN GYEIFPQLKF ERPGEKEEID PYVCFRRREV RHP RKTRRI DILNSQRLRA LHQELKNAKD LALLVAKREN VSLNWINDEL KIFDQRVKIK NLKRSLNISG EDDDLINHKR KRPT IVTVE QREAELRKAE LKRAAAAAAA AKAKNNKRNN QLEDKSSRLT KQQQQQLLQQ QQQQQQNALK TENGKQLANA SSSST SQPI TSHVYVKLPS SKIPDIVLED VDALLNSKEK NARKFVQEKM EKRKIEDADV FFNLTDDPFN PVFDMSLPKN FSTSNV PFA SIASSKFQID RSFYSSHLPE YLKGISDDIR IYDSNGRSRN KDNYNLDTKR IKKTELYDPF QENLEIHSRE YPIKFRK RV GRSNIKYVDR MPNFTTSSTK SACSLMDFVD FDSIEKEQYS REGSNDTDSI NVYDSKYDEF VRLYDKWKYD SPQNEYGI K FSDEPARLNQ ISNDTQVIRF GTMLGTKSYE QLREATIKYR RDYITRLKQK HIQHLQQQQQ QQQQQQQQAQ QQKQKSQNN NSNSSNSLKK LNDSLINSEA KQNSSITQKN SS

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Macromolecule #4: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.435126 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVALFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

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Macromolecule #5: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

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Macromolecule #6: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 14.109436 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVR NDEELNKLLG RVTIAQGGVL PNIQSVLLPK KTESSKSAKS K

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Macromolecule #7: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.965265 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KTQKKDGKKR RKSRKESYAI YVYKVLKQVH PDTGISSKAM SIMNSFVNDV FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK

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Macromolecule #8: Histone acetyltransferase ESA1

MacromoleculeName: Histone acetyltransferase ESA1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 52.692844 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSHDGKEEPG IAKKINSVDD IIIKCQCWVQ KNDEERLAEI LSINTRKAPP KFYVHYVNYN KRLDEWITTD RINLDKEVLY PKLKATDED NKKQKKKKAT NTSETPQDSL QDGVDGFSRE NTDVMDLDNL NVQGIKDENI SHEDEIKKLR TSGSMTQNPH E VARVRNLN ...String:
MSHDGKEEPG IAKKINSVDD IIIKCQCWVQ KNDEERLAEI LSINTRKAPP KFYVHYVNYN KRLDEWITTD RINLDKEVLY PKLKATDED NKKQKKKKAT NTSETPQDSL QDGVDGFSRE NTDVMDLDNL NVQGIKDENI SHEDEIKKLR TSGSMTQNPH E VARVRNLN RIIMGKYEIE PWYFSPYPIE LTDEDFIYID DFTLQYFGSK KQYERYRKKC TLRHPPGNEI YRDDYVSFFE ID GRKQRTW CRNLCLLSKL FLDHKTLYYD VDPFLFYCMT RRDELGHHLV GYFSKEKESA DGYNVACILT LPQYQRMGYG KLL IEFSYE LSKKENKVGS PEKPLSDLGL LSYRAYWSDT LITLLVEHQK EITIDEISSM TSMTTTDILH TAKTLNILRY YKGQ HIIFL NEDILDRYNR LKAKKRRTID PNRLIWKPPV FTASQLRFAW

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Macromolecule #11: Epl1 arginine anchor

MacromoleculeName: Epl1 arginine anchor / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 1.175449 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
FRHRKISVK

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Macromolecule #12: Chromatin modification-related protein EAF1

MacromoleculeName: Chromatin modification-related protein EAF1 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 133.949953 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSSRPSSAVP NSASLSEDQS SDRSKFPKAD DLIDERDRKL TELYCVSRLN QLLELTDENK LRKEIDAFLK KNDIRRGIRF DEASLPKLL HTAATPITKK KLKDVNLINV PNQRLSDSKM SRELPENSEN VSVKSESHFV PSHDNSIREN MMDSLRPAEK T GGMWNKRP ...String:
MSSRPSSAVP NSASLSEDQS SDRSKFPKAD DLIDERDRKL TELYCVSRLN QLLELTDENK LRKEIDAFLK KNDIRRGIRF DEASLPKLL HTAATPITKK KLKDVNLINV PNQRLSDSKM SRELPENSEN VSVKSESHFV PSHDNSIREN MMDSLRPAEK T GGMWNKRP LESTMGGEEE RHEKRQKMQS QSLESSNNSE MASLPISPRP PVPNALAHYT YYENIEYPPA DPTEVQPAVK FK DPLIKNI MAKEIDTSDH YNENNVDALE TVFLLMNDYI PSKIPQALPL AELKYMSQTL PLINLIPRAH KALTTNIINN ALN EARITV VGSRIEELRR LGLWSLRQPK RFIDPWKQHN THQNILLEEA KWMQADFKEG HKYKVAICTA MAQAIKDYWT YGEI CCVKR KTLLPGKENK LSDDGRISEK SGRPSDTSRN DSDISIAGKD DIGIIANVDD ITEKESAAAN DNDENGKNEA GAKSD FDFA DGLLSQEGAH DQIISSIDTK LLLKKPSSSS EVVLIQHEVA ASSALIETEE SKKELAPPFK LSIFVDELNT FEKTLI QDL PLYNGINEER PKKDDSLPFI PISKSVVSLD DNGFYKLLER QLIDEEPSIS QLSKRRGMFY GNRRNHYLRP PAVPSLR YL QNRTPTIWLS EDDQELVKNI NTYGYNWELI SAHMTHRLTY SYLSNIERRT PWQCFERFVQ LNERFNFSDL KGPRAHSA Q QWLIEAHKFQ QRQNRRISPL GVNTESIQRG HRRLRWASMF EAIRKCMKKR ENTPRPNPTQ PRKPLDCKNM KVPTPAEMS LLKAQRDEAL RRDIQLRRTV KNRLQQRQQQ SQQAHSSRAQ SPIPSNGKSS SNLARNGQAS APRPNQKQYT EQDIIESYSR KLLEQKPDI GPEMALKAAK NYYRTLREQQ QQLKQHQIQQ QRQQLQEESS HVQQLQQLQP GSQAPPPKSS PSQSSLSNIS N INSAPRIK SPTPQEILQR FQKQRTLQVD WSHPQFEKHH HHHHHHHHHH DYDIPTTASV DGSENLYFQG SPQQNKTAAL AQ HDEAVDN KFNKEQQNAF YEILHLPNLN EEQRNAFIQS LKDDPSQSAN LLAEAKKLND AQAPKVDNKF NKEQQNAFYE ILH LPNLNE EQRNAFIQSL KDDPSQSANL LAEAKKLNDA QAPKVDANSA AL

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Macromolecule #13: Actin-related protein 4

MacromoleculeName: Actin-related protein 4 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 54.894684 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSNAALQVYG GDEVSAVVID PGSYTTNIGY SGSDFPQSIL PSVYGKYTAD EGNKKIFSEQ SIGIPRKDYE LKPIIENGLV IDWDTAQEQ WQWALQNELY LNSNSGIPAL LTEPVWNSTE NRKKSLEVLL EGMQFEACYL APTSTCVSFA AGRPNCLVVD I GHDTCSVS ...String:
MSNAALQVYG GDEVSAVVID PGSYTTNIGY SGSDFPQSIL PSVYGKYTAD EGNKKIFSEQ SIGIPRKDYE LKPIIENGLV IDWDTAQEQ WQWALQNELY LNSNSGIPAL LTEPVWNSTE NRKKSLEVLL EGMQFEACYL APTSTCVSFA AGRPNCLVVD I GHDTCSVS PIVDGMTLSK STRRNFIAGK FINHLIKKAL EPKEIIPLFA IKQRKPEFIK KTFDYEVDKS LYDYANNRGF FQ ECKETLC HICPTKTLEE TKTELSSTAK RSIESPWNEE IVFDNETRYG FAEELFLPKE DDIPANWPRS NSGVVKTWRN DYV PLKRTK PSGVNKSDKK VTPTEEKEQE AVSKSTSPAA NSADTPNETG KRPLEEEKPP KENNELIGLA DLVYSSIMSS DVDL RATLA HNVVLTGGTS SIPGLSDRLM TELNKILPSL KFRILTTGHT IERQYQSWLG GSILTSLGTF HQLWVGKKEY EEVGV ERLL NDRFR

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Macromolecule #14: Actin

MacromoleculeName: Actin / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 41.735547 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MDSEVAALVI DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGIMVGMGQK DSYVGDEAQS KRGILTLRYP IEHGIVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP MNPKSNREKM TQIMFETFNV PAFYVSIQAV LSLYSSGRTT GIVLDSGDGV T HVVPIYAG ...String:
MDSEVAALVI DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGIMVGMGQK DSYVGDEAQS KRGILTLRYP IEHGIVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP MNPKSNREKM TQIMFETFNV PAFYVSIQAV LSLYSSGRTT GIVLDSGDGV T HVVPIYAG FSLPHAILRI DLAGRDLTDY LMKILSERGY SFSTTAEREI VRDIKEKLCY VALDFEQEMQ TAAQSSSIEK SY ELPDGQV ITIGNERFRA PEALFHPSVL GLESAGIDQT TYNSIMKCDV DVRKELYGNI VMSGGTTMFP GIAERMQKEI TAL APSSMK VKIIAPPERK YSVWIGGSIL ASLTTFQQMW ISKQEYDESG PSIVHHKCF

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Macromolecule #15: SWR1-complex protein 4

MacromoleculeName: SWR1-complex protein 4 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 55.297684 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSSSDIFDVL NIKQKSRSPT NGQVSVPSSS AANRPKPQVT GMQRELFNLL GENQPPVVIK SGNNFKEKML STSKPSPWSF VEFKANNSV TLRHWVKGSK ELIGDTPKES PYSKFNQHLS IPSFTKEEYE AFMNENEGTQ KSVESEKNHN ENFTNEKKDE S KNSWSFEE ...String:
MSSSDIFDVL NIKQKSRSPT NGQVSVPSSS AANRPKPQVT GMQRELFNLL GENQPPVVIK SGNNFKEKML STSKPSPWSF VEFKANNSV TLRHWVKGSK ELIGDTPKES PYSKFNQHLS IPSFTKEEYE AFMNENEGTQ KSVESEKNHN ENFTNEKKDE S KNSWSFEE IEYLFNLCKK YDLRWFLIFD RYSYNNSRTL EDLKEKFYYT CRNYFKASDP SNPLLSSLNF SAEKEIERKK YL QRLLSRS AAEIAEEEAL VVESKKFEMA AKRTLAERES LLRLLDSPHS DQTITQYLTS QGMSQLYNAL LADKTRKRKH DLN IPENPW MKQQQQFAQH RQLQQLNVKK SEVKENLSPK KTKRQRQEMQ TALKRKSESA YAEQLLKDFN SDERKALGVI THGE KLSPG VYLRSTKLST FKPALQNKIL AILQELSLPS RPVMPSFDVM ERQEELLKKI NTLIDLKKHV DKYEAGMSIT K

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Macromolecule #16: Transcription-associated protein 1

MacromoleculeName: Transcription-associated protein 1 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 433.677281 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSLTEQIEQF ASRFRDDDAT LQSRYSTLSE LYDIMELLNS PEDYHFFLQA VIPLLLNQLK EVPISYDAHS PEQKLRNSML DIFNRCLMN QTFQPYAMEV LEFLLSVLPK ENEENGILCM KVLTTLFKSF KSILQDKLDS FIRIIIQIYK NTPNLINQTF Y EAGKAEQG ...String:
MSLTEQIEQF ASRFRDDDAT LQSRYSTLSE LYDIMELLNS PEDYHFFLQA VIPLLLNQLK EVPISYDAHS PEQKLRNSML DIFNRCLMN QTFQPYAMEV LEFLLSVLPK ENEENGILCM KVLTTLFKSF KSILQDKLDS FIRIIIQIYK NTPNLINQTF Y EAGKAEQG DLDSPKEPQA DELLDEFSKN DEEKDFPSKQ SSTEPRFENS TSSNGLRSSM FSFKILSECP ITMVTLYSSY KQ LTSTSLP EFTPLIMNLL NIQIKQQQEA REQAESRGEH FTSISTEIIN RPAYCDFILA QIKATSFLAY VFIRGYAPEF LQD YVNFVP DLIIRLLQDC PSELSSARKE LLHATRHILS TNYKKLFLPK LDYLFDERIL IGNGFTMHET LRPLAYSTVA DFIH NIRSE LQLSEIEKTI KIYTGYLLDE SLALTVQIMS AKLLLNLVER ILKLGKENPQ EAPRAKKLLM IIIDSYMNRF KTLNR QYDT IMKYYGRYET HKKEKAEKLK NSIQDNDKES EEFMRKVLEP SDDDHLMPQP KKEDINDSPD VEMTESDKVV KNDVEM FDI KNYAPILLLP TPTNDPIKDA FYLYRTLMSF LKTIIHDLKV FNPPPNEYTV ANPKLWASVS RVFSYEEVIV FKDLFHE CI IGLKFFKDHN EKLSPETTKK HFDISMPSLP VSATKDAREL MDYLAFMFMQ MDNATFNEII EQELPFVYER MLEDSGLL H VAQSFLTSEI TSPNFAGILL RFLKGKLKDL GNVDFNTSNV LIRLFKLSFM SVNLFPNINE VVLLPHLNDL ILNSLKYST TAEEPLVYFY LIRTLFRSIG GGRFENLYRS IKPILQVLLQ SLNQMILTAR LPHERELYVE LCITVPVRLS VLAPYLPFLM KPLVFALQQ YPDLVSQGLR TLELCIDNLT AEYFDPIIEP VIDDVSKALF NLLQPQPFNH AISHNVVRIL GKLGGRNRQF L KPPTDLTE KTELDIDAIA DFKINGMPED VPLSVTPGIQ SALNILQSYK SDIHYRKSAY KYLTCVLLLM TKSSAEFPTN YT ELLKTAV NSIKLERIGI EKNFDLEPTV NKRDYSNQEN LFLRLLESVF YATSIKELKD DAMDLLNNLL DHFCLLQVNT TLL NKRNYN GTFNIDLKNP NFMLDSSLIL DAIPFALSYY IPEVREVGVL AYKRIYEKSC LIYGEELALS HSFIPELAKQ FIHL CYDET YYNKRGGVLG IKVLIDNVKS SSVFLKKYQY NLANGLLFVL KDTQSEAPSA ITDSAEKLLI DLLSITFADV KEEDL GNKV LENTLTDIVC ELSNANPKVR NACQKSLHTI SNLTGIPIVK LMDHSKQFLL SPIFAKPLRA LPFTMQIGNV DAITFC LSL PNTFLTFNEE LFRLLQESIV LADAEDESLS TNIQKTTEYS TSEQLVQLRI ACIKLLAIAL KNEEFATAQQ GNIRIRI LA VFFKTMLKTS PEIINTTYEA LKGSLAENSK LPKELLQNGL KPLLMNLSDH QKLTVPGLDA LSKLLELLIA YFKVEIGR K LLDHLTAWCR VEVLDTLFGQ DLAEQMPTKI IVSIINIFHL LPPQADMFLN DLLLKVMLLE RKLRLQLDSP FRTPLARYL NRFHNPVTEY FKKNMTLRQL VLFMCNIVQR PEAKELAEDF EKELDNFYDF YISNIPKNQV RVVSFFTNMV DLFNTMVITN GDEWLKKKG NMILKLKDML NLTLKTIKEN SFYIDHLQLN QSIAKFQALY LRFTELSERD QNPLLLDFID FSFSNGIKAS Y SLKKFIFH NIIASSNKEK QNNFINDATL FVLSDKCLDA RIFVLKNVIN STLIYEVATS GSLKSYLVED KKPKWLELLH NK IWKNSNA ILAYDVLDHH DLFRFELLQL SAIFIKADPE IIAEIKKDII KFCWNFIKLE DTLIKQSAYL VTSYFISKFD FPI KVVTQV FVALLRSSHV EARYLVKQSL DVLTPVLHER MNAAGTPDTW INWVKRVMVE NSSSQNNILY QFLISHPDLF FNSR DLFIS NIIHHMNKIT FMSNSNSDSH TLAIDLASLI LYWENKTLEI TNVNNTKTDS DGDVVMSDSK SDINPVEADT TAIIV DANN NSPISLHLRE ACTAFLIRYV CASNHRAIET ELGLRAINIL SELISDKHWT NVNVKLVYFE KFLIFQDLDS ENILYY CMN ALDVLYVFFK NKTKEWIMEN LPTIQNLLEK CIKSDHHDVQ EALQKVLQVI MKAIKAQGVS VIIEEESPGK TFIQMLT SV ITQDLQETSS VTAGVTLAWV LFMNFPDNIV PLLTPLMKTF SKLCKDHLSI SQPKDAMALE EARITTKLLE KVLYILSL K VSLLGDSRRP FLSTVALLID HSMDQNFLRK IVNMSRSWIF NTEIFPTVKE KAAILTKMLA FEIRGEPSLS KLFYEIVLK LFDQEHFNNT EITVRMEQPF LVGTRVEDIG IRKRFMTILD NSLERDIKER LYYVIRDQNW EFIADYPWLN QALQLLYGSF NREKELSLK NIYCLSPPSI LQEYLPENAE MVTEVNDLEL SNFVKGHIAS MQGLCRIISS DFIDSLIEIF YQDPKAIHRA W VTLFPQVY KSIPKNEKYG FVRSIITLLS KPYHTRQISS RTNVINMLLD SISKIESLEL PPHLVKYLAI SYNAWYQSIN IL ESIQSNT SIDNTKIIEA NEDALLELYV NLQEEDMFYG LWRRRAKYTE TNIGLSYEQI GLWDKAQQLY EVAQVKARSG ALP YSQSEY ALWEDNWIQC AEKLQHWDVL TELAKHEGFT DLLLECGWRV ADWNSDRDAL EQSVKSVMDV PTPRRQMFKT FLAL QNFAE SRKGDQEVRK LCDEGIQLSL IKWVSLPIRY TPAHKWLLHG FQQYMEFLEA TQIYANLHTT TVQNLDSKAQ EIKRI LQAW RDRLPNTWDD VNMWNDLVTW RQHAFQVINN AYLPLIPALQ QSNSNSNINT HAYRGYHEIA WVINRFAHVA RKHNMP DVC ISQLARIYTL PNIEIQEAFL KLREQAKCHY QNMNELTTGL DVISNTNLVY FGTVQKAEFF TLKGMFLSKL RAYEEAN QA FATAVQIDLN LAKAWAQWGF FNDRRLSEEP NNISFASNAI SCYLQAAGLY KNSKIRELLC RILWLISIDD ASGMLTNA F DSFRGEIPVW YWITFIPQLL TSLSHKEANM VRHILIRIAK SYPQALHFQL RTTKEDFAVI QRQTMAVMGD KPDTNDRNG RRQPWEYLQE LNNILKTAYP LLALSLESLV AQINDRFKST TDEDLFRLIN VLLIDGTLNY NRLPFPRKNP KLPENTEKNL VKFSTTLLA PYIRPKFNAD FIDNKPDYET YIKRLRYWRR RLENKLDRAS KKENLEVLCP HLSNFHHQKF EDIEIPGQYL L NKDNNVHF IKIARFLPTV DFVRGTHSSY RRLMIRGHDG SVHSFAVQYP AVRHSRREER MFQLYRLFNK SLSKNVETRR RS IQFNLPI AIPLSPQVRI MNDSVSFTTL HEIHNEFCKK KGFDPDDIQD FMADKLNAAH DDALPAPDMT ILKVEIFNSI QTM FVPSNV LKDHFTSLFT QFEDFWLFRK QFASQYSSFV FMSYMMMINN RTPHKIHVDK TSGNVFTLEM LPSRFPYERV KPLL KNHDL SLPPDSPIFH NNEPVPFRLT PNIQSLIGDS ALEGIFAVNL FTISRALIEP DNELNTYLAL FIRDEIISWF SNLHR PIIE NPQLREMVQT NVDLIIRKVA QLGHLNSTPT VTTQFILDCI GSAVSPRNLA RTDVNFMPWF

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Macromolecule #9: DNA (207-mer)

MacromoleculeName: DNA (207-mer) / type: dna / ID: 9 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 63.679512 KDa
SequenceString: (DT)(DC)(DC)(DG)(DG)(DA)(DG)(DG)(DA)(DC) (DT)(DG)(DT)(DC)(DC)(DT)(DC)(DC)(DG)(DG) (DG)(DG)(DA)(DC)(DC)(DC)(DT)(DA)(DT) (DA)(DC)(DG)(DC)(DG)(DG)(DC)(DC)(DG)(DC) (DC) (DA)(DT)(DC)(DG)(DA)(DG) ...String:
(DT)(DC)(DC)(DG)(DG)(DA)(DG)(DG)(DA)(DC) (DT)(DG)(DT)(DC)(DC)(DT)(DC)(DC)(DG)(DG) (DG)(DG)(DA)(DC)(DC)(DC)(DT)(DA)(DT) (DA)(DC)(DG)(DC)(DG)(DG)(DC)(DC)(DG)(DC) (DC) (DA)(DT)(DC)(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) (DA)(DC)(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)(DG)(DA)(DT)(DA)(DG)(DC)(DT) (DT)(DG)(DT)(DC)(DG)(DA)(DG)(DA)(DA) (DG)(DT)(DA)(DC)(DT)(DA)(DG)

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Macromolecule #10: DNA (207-mer)

MacromoleculeName: DNA (207-mer) / type: dna / ID: 10 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 64.150809 KDa
SequenceString: (DC)(DT)(DA)(DG)(DT)(DA)(DC)(DT)(DT)(DC) (DT)(DC)(DG)(DA)(DC)(DA)(DA)(DG)(DC)(DT) (DA)(DT)(DC)(DG)(DG)(DA)(DT)(DG)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA) (DC) (DA)(DC)(DG)(DT)(DG)(DC) ...String:
(DC)(DT)(DA)(DG)(DT)(DA)(DC)(DT)(DT)(DC) (DT)(DC)(DG)(DA)(DC)(DA)(DA)(DG)(DC)(DT) (DA)(DT)(DC)(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)(DG)(DT)(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)(DG)(DA)(DT)(DG)(DG)(DC)(DG)(DG) (DC)(DC)(DG)(DC)(DG)(DT)(DA)(DT) (DA) (DG)(DG)(DG)(DT)(DC)(DC)(DC)(DC)(DG)(DG) (DA)(DG)(DG)(DA)(DC)(DA)(DG)(DT)(DC) (DC)(DT)(DC)(DC)(DG)(DG)(DA)

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Macromolecule #17: CARBOXYMETHYL COENZYME *A

MacromoleculeName: CARBOXYMETHYL COENZYME *A / type: ligand / ID: 17 / Number of copies: 1 / Formula: CMC
Molecular weightTheoretical: 825.57 Da
Chemical component information

ChemComp-CMC:
CARBOXYMETHYL COENZYME *A

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Macromolecule #18: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 18 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #19: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 19 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

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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

BufferpH: 7.6
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.3 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2

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Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 474949

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