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- EMDB-14989: NuA4 Histone Acetyltransferase Complex (Composite) -

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Basic information

Entry
Database: EMDB / ID: EMD-14989
TitleNuA4 Histone Acetyltransferase Complex (Composite)
Map dataPrimary Map
Sample
  • Complex: NuA4 histone acetyltransferase complex
    • Protein or peptide: Transcription-associated protein
    • Protein or peptide: Actin
    • Protein or peptide: Actin
    • Protein or peptide: Chromatin modification-related protein EAF1
    • Protein or peptide: SWR1-complex protein 4
    • Protein or peptide: Enhancer of polycomb-like protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsNuA4 / histone acetyltransferase complex / Epigenetics / DNA repair / TRANSCRIPTION
Function / homology
Function and homology information


: / : / piccolo histone acetyltransferase complex / : / Swr1 complex / kinetochore assembly / Ino80 complex / SAGA complex / NuA4 histone acetyltransferase complex / positive regulation of macroautophagy ...: / : / piccolo histone acetyltransferase complex / : / Swr1 complex / kinetochore assembly / Ino80 complex / SAGA complex / NuA4 histone acetyltransferase complex / positive regulation of macroautophagy / chromosome organization / histone acetyltransferase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / nucleosome / chromatin organization / histone binding / cytoskeleton / hydrolase activity / chromatin remodeling / DNA repair / DNA damage response / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / ATP binding / nucleus / cytoplasm
Similarity search - Function
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 / Myb-like domain profile. / domain in helicases and associated with SANT domains ...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 / Myb-like domain profile. / domain in helicases and associated with SANT domains / Myb-like DNA-binding domain / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / 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 / Homeobox-like domain superfamily / ATPase, nucleotide binding domain / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Actin / Transcription-associated protein / SWR1-complex protein 4 / Enhancer of polycomb-like protein / Chromatin modification-related protein EAF1 / Actin
Similarity search - Component
Biological speciesKomagataella phaffii GS115 (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsSchultz P / Ben-Shem A / Frechard A / Papai G / Smirnova E / Faux C / Lo Ying Ping F / Helmlinger D / Ben-shem A
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE12-0022 France
Citation
Journal: Nat Struct Mol Biol / Year: 2023
Title: The structure of the NuA4-Tip60 complex reveals the mechanism and importance of long-range chromatin modification.
Authors: Alexander Fréchard / Céline Faux / Rozalie Hexnerova / Corinne Crucifix / Gabor Papai / Ekaterina Smirnova / Conor McKeon / Florie Lo Ying Ping / Dominique Helmlinger / Patrick Schultz / Adam Ben-Shem /
Abstract: Histone acetylation regulates most DNA transactions and is dynamically controlled by highly conserved enzymes. The only essential histone acetyltransferase (HAT) in yeast, Esa1, is part of the 1-MDa ...Histone acetylation regulates most DNA transactions and is dynamically controlled by highly conserved enzymes. The only essential histone acetyltransferase (HAT) in yeast, Esa1, is part of the 1-MDa NuA4 complex, which plays pivotal roles in both transcription and DNA-damage repair. NuA4 has the unique capacity to acetylate histone targets located several nucleosomes away from its recruitment site. Neither the molecular mechanism of this activity nor its physiological importance are known. Here we report the structure of the Pichia pastoris NuA4 complex, with its core resolved at 3.4-Å resolution. Three subunits, Epl1, Eaf1 and Swc4, intertwine to form a stable platform that coordinates all other modules. The HAT module is firmly anchored into the core while retaining the ability to stretch out over a long distance. We provide structural, biochemical and genetic evidence that an unfolded linker region of the Epl1 subunit is critical for this long-range activity. Specifically, shortening the Epl1 linker causes severe growth defects and reduced H4 acetylation levels over broad chromatin regions in fission yeast. Our work lays the foundations for a mechanistic understanding of NuA4's regulatory role and elucidates how its essential long-range activity is attained.
#1: Journal: Res Sq / Year: 2022
Title: The structure of the NuA4/Tip60 complex reveals the mechanism and importance of long-range chromatin modification
Authors: Schultz P / Frechard A / Hexnerova R / Crucifix C / Papai G / Smirnova E / Faux C / Ping F / Helmlinger D / Ben-Shem A
History
DepositionMay 17, 2022-
Header (metadata) releaseMay 31, 2023-
Map releaseMay 31, 2023-
UpdateSep 20, 2023-
Current statusSep 20, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14989.png

Downloads & links

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Map

FileDownload / File: emd_14989.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 448 pix.
= 386.176 Å		0.86 Å/pix.
x 448 pix.
= 386.176 Å		0.86 Å/pix.
x 448 pix.
= 386.176 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.862 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-2.1877048 - 4.0050635
Average (Standard dev.)0.004822786 (±0.062332164)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 386.176 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : NuA4 histone acetyltransferase complex

EntireName: NuA4 histone acetyltransferase complex
Components
  • Complex: NuA4 histone acetyltransferase complex
    • Protein or peptide: Transcription-associated protein
    • Protein or peptide: Actin
    • Protein or peptide: Actin
    • Protein or peptide: Chromatin modification-related protein EAF1
    • Protein or peptide: SWR1-complex protein 4
    • Protein or peptide: Enhancer of polycomb-like protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: NuA4 histone acetyltransferase complex

SupramoleculeName: NuA4 histone acetyltransferase complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Komagataella phaffii GS115 (fungus)

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Macromolecule #1: Transcription-associated protein

MacromoleculeName: Transcription-associated protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii GS115 (fungus) / Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 438.055344 KDa
SequenceString: MLHVVQLDDF ATRLKAAEDY QSKHSVLSEI CDSLETFNAA QDYEYFLKSL IPLFIDVLKE VPVSFVANSP ENKLRNITLE ILHRIPAND ALQAYSNEIV DTLMDLLKVE NELNGILCMK AITTLHKTFK ASLQEKVHPF IDIVIEIYSN IPQVVEEQFN G NQIDSKEN ...String:
MLHVVQLDDF ATRLKAAEDY QSKHSVLSEI CDSLETFNAA QDYEYFLKSL IPLFIDVLKE VPVSFVANSP ENKLRNITLE ILHRIPAND ALQAYSNEIV DTLMDLLKVE NELNGILCMK AITTLHKTFK ASLQEKVHPF IDIVIEIYSN IPQVVEEQFN G NQIDSKEN VDSTSRPNSP SFSSQSDDSK QLAQAMFSFK TLAESPITMV SLYSSYKELA ASSLGNFIPH VMKVLSLEVA KQ AEARKAA EEKGIILVNV CKEITNRANY GEFIIGQVKA ASFLAYLFIR RQAQTFLEPY QQAIPDIIIR LLQDCPSELS AAR KELLHA TRHILSTDFR KMFIPKIDLL FDLRVLIGEG FTAYETLRPL AYSTVADFIH NVRDHLTPAQ LWKSVSIYCK NLQD DSLAL TVQIMSAKLL LNLIEKIMRS ESKTESRQLL MVIIDAYTKR FKMLNSRYNG IMKQHATYEK EKQEKQNQER LLTNK LDGT TPSPSDDKKV ELIDEDQDVK MEDPTPEISD QETIKGDNDA STEPQDSEQQ LADFMSLQEY LPIQVSVPPE IDLLKD SRY LFKTLMTFLK TIMIGLKNSN PPSSQNHFNA QNWNETARGF SNEDINILKS LFRECILALR FFSTSKTSLP ASSMKQS FD ITGPNLPITS TKEEKDLMEI FATMFIHIDP ASFNEIVREE LPFMYKQMLD FASLLHIPQF FLASVITSSS FSGILITF L KSKLVDLGEV NIIKSNILIR LFKLCFMSVS LFPAANESVI LPHLNELILK SLKLSTTAKE PLVYFYLIRT LFRSIGGGR FENLYKEIMP LLQVLLESLS KLIHEARRPQ ERDIYVELCL TVPVRLSVLV PHLSYLMKPL VYALNGSQES VSQGLRTLEL CVDNLTAEY FDPIIEPVID DVMEALSKHL KPLPYYHQHS HTTLRILGKL GGRNRTFIKP VDNLKTDSEL FQNVEAMFKI H GLPNEVPL SITPGLSAAF SLLTDPRPRI HYRINSFKYI SGIFQLFLGA TQLPDDYANR LKESMDIILE DTIAPDEPLN KL HHFPVKD IAKYDSQMEL LVKLLESIFY AVSLQEVREE SKALIRGTCN HFILLYFNKM VIDKRKFVRK FSVDNHEGNL FLN ENCIFD AIIYALSSDN SAVRSMGLES VQLIYDSCVE LFGNIDCALK FAPLNVMCSK FIHCCFEEPY HKKLAGCIGL EMML NSLDI PMKYFNARQL EIIRALFYVL RDTAPELPCE VTNTAKRLIL NSLKEWNKEL TRNDVFSSVF QNLVSSLIVD LPNAN EIVR ATAQEALRTL SETTQVPIAT MISPCKHILL APIFGKPLRA LPFQMQIGNI DAITFCMGLE NSFLEYNEEL NRLVQE ALA LVDAEDESLV SAHRISEHKT SEQLVRLRVV CIQLLSLAIT KPEFAAAQQR SNIRVKILVV FFKSLCGRSI EIIRAAH GG LKAVIDLKMK LPKELLQNGL RPMLMNLSDH KKLTVASLEA LSGLLKLFIS YFKVGIGSKL LDHLLAWAQP RTLQQLGS Q DLENNSTVQI IVAILDVFHL LPPTAHKFMN DLMNALLYLE NNLHRCQYSP FREPLAKFLD RFPDESFEYF FNEFSKREI TTRFVYFVGL DSCSSLRAKV LESLPRVRGL LHQEGSAEEK CVRFSNLVDL CESLAASDKE WIKDKEELLG ELLDAGSVCL TLKRSSNVV SPLYFQVDQG FETLQLLYIE YFKSQPLGHE KVFNFIDKIS KEGLPFVLEF DDFIFNEVVK CQDIPTVQQT L DTIIRMTP QVSSLDARVY LYKRIFLPIC IYESEMHGDL SRLSQTENNE LPAWLKSFDS DVWKATGPLV DDYTSTLEDR YR LELMQLT ALLIKGAPTA LTDMRKDIIK FSWNYIKLDD NTSKQAAYVV TAYFISRFDT PSELTTRIFV ALLRCHQIDT RYL VKQALE LLAPVLSERT NSELDWLKWP RRVLSEDGFN ITQVANIYQL IVKFPDLFYP ARDHFIPNII TAMGKLTVMS NTSL ENQQL AIDLAELILK WETKLPKSEK LGSAEETEKE KSVSEDKMDI DVKEETKEDI AERPKAEDQI GGDDSDSSNI LTSED YEVS FAQREACVTF LIRYICISTQ RPSENELGKR ALNILYELLG PKYWSEVTVK LQFFERFLMS SDLNQPSLLG YCLNAL EVL AVALKWKPTT WIIENVSYLQ KLLEKCLRSD NQDIQEILQK VLGIILEAIN KETQGSEEDE PEEVTNFISL IVNIIGE DL SNMTSVAAGV SLCWTLSLYR PNALDSLLPS IMRTFNKLCR DHIAISLQGN QPQSGDFANI EFEAKVTTNL LEKILNLC A ARISSLDDQR RVFLSLLAQL IDRSVDKDML LKVINIVTEW IFKTDFYPTT KEKAGILGKM MIFDLRGEPE LSKKFNQVI VDIFESKELA HTELTARMET AFLFGTRLSD VSIRKKLMSI LSDSLELDID KRLFYIIKDQ NWEYLSDYPW LNQALQLLYG SFHLDSPIR LSPEENTLSP LQSITEGLAR EKSPVEKAPQ NIIDFVAKHN EFLDSVRSLT AGDILNPLID ISYQSAETIH N AWVVVFPV AYSAIESRYE LEFTRALVKL LFKDYHIRQQ DARPNVIKSL LDGVGKCPGL HLPPHLVKYL GSNYNAWYGA IK LLEELSE GQGIDNQKIS DANQDALLEV YMSLQEDDMF YGTWRRRAKY FETNAALSYE QIGIWDKALQ LYEAAQIKAR SGV FPFGES EYSLWEDHWI YCAEKLQHWE ILTELAKHEG FTDLLLECGW RGADWIADRE PLEQSVKTVM DIPTPRRQIF QTFL ALQGF SQQKDTLQDV SRLCDEGIQL TLRKWNALPQ RVTRAHIGLL HTFQQYVELM EASQVYSSLV TTNAQNLDVK SQELK RVLQ AWRERLPNVW DDINIWNDLV TWRQHVFGVI NRVYMPFVPV LQQSNGTNNG NSYAYRGYHE MAWVINRFAH VARKHE MPE VCINQLTKIY TLPNIEIQEA FLKLREQAKC HYQNSSELNT GLDVISNTNL VYFATQQKAE FFTLKGMFLA KLNAKDE AN QAFATAVQID LNLPKAWAEW GFFNDRRFKE NPEEIFHAKN AISCYLQAAG LYKDGKTRKL LCRILWLISL DDAAGSLA K TFEDHHGESP VWYWITFVPQ LLTSLSHKEA KIVRHILIQI AKSYPQSLHF QLRTTKEDYQ AIQRQAMAVN RAEEQSSNK QDTADSVLKN TNTPQPQTRT ETSGTTAESD KKPSIPPKEE QGSPQPSRPA TTQASPQAQS QENGESSQKH PPEIPTTDSR QPWQDVEEI MGILKTAYPL LALSLESLVD QLNQRFKCNA DEDAYRLVIV LYNDGVQQMN RVANPREEVK LPAATEASIS R FADSVLPK NIREVFEQDI IACNPNLETY ISKLRKWRDC LEEKLDRSYG KADLERVSLH LSLFHHQKFE DIEIPGQYLL HK DNNNHFI KIERFLPTLD LVRGSNGCYK RMTIRGNDGS LHPFAVQFPA ARHCRREERI FQLFRIFDDA LSRKVQSRRR NIS LTLPIA VPLSPHIRIL NDDKRYTTLM GIYEEFCRRK GQSRDEPFAY TIQKLRAAFD PRLPKPDIVS VRAEVLASIQ STLV PSTLL KDYYTEKFSN YENYWLFRKQ FTAQYASFIF MTYIMCINSR QPQKIHINEG SGNIWTSEML PTKVATGKTH STAYN NSTL DPAVKAGAPI FYNTESVPFR LTPNIQKFIG EAGLEGILSV YILVIANSLS DSEFDMEQYL SLFVRDEVIS WFAQQH RAS AQTNQLREIV RVNVELLTKR VLQLNHIPNS QNVATQFVLN LISQAVNPRN LAYTDSAWMA YL

UniProtKB: Transcription-associated protein

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Macromolecule #2: Actin

MacromoleculeName: Actin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii GS115 (fungus) / Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 41.736406 KDa
SequenceString: MDGEDVAALV IDNGSGMCKA GYAGDDAPHT VFPSVVGRPR HQGVMVGMGQ KDSFVGDEAQ SKRGILTLRY PIEHGIVTNW DDMEKIWHH TFYNELRLAP EEHPVLLTEA PMNPKSNREK MTQIMFETFN VPAFYVSIQA VLSLYASGRT TGIVLDSGDG V THVVPIYA ...String:
MDGEDVAALV IDNGSGMCKA GYAGDDAPHT VFPSVVGRPR HQGVMVGMGQ KDSFVGDEAQ SKRGILTLRY PIEHGIVTNW DDMEKIWHH TFYNELRLAP EEHPVLLTEA PMNPKSNREK MTQIMFETFN VPAFYVSIQA VLSLYASGRT TGIVLDSGDG V THVVPIYA GFSLPHAILR IDLAGRDLTD YLMKILSERG YTFSTSAERE IVRDIKEKLC YVALDFDQEL QTSSQSSSIE KS YELPDGQ VITIGNERFR APEALFHPSV LGLEASGIDQ TTYNSIMKCD VDVRKELYSN IVMSGGTTMF PGIAERMQKE LTA LAPSSM KVKISAPPER KYSVWIGGSI LASLGTFQQM WISKQEYDES GPSIVHLKCF

UniProtKB: Actin

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Macromolecule #3: Actin

MacromoleculeName: Actin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii GS115 (fungus) / Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 53.009074 KDa
SequenceString: MATAPQVYGA DEINAVVLDA SSYRTKIGYG SLDCPILNLP SYYGHQTKDG SEKFIFEENS MLIPRPDYEI KKIMKDGIID DFEGAVKQY NYMFDVLKLK PSEQPILVIE STQNEYEKKT ALLKQLLKEN KFVATFLIKN PTCVSFAHGR PNCLVVDLGH D LVTITPIL ...String:
MATAPQVYGA DEINAVVLDA SSYRTKIGYG SLDCPILNLP SYYGHQTKDG SEKFIFEENS MLIPRPDYEI KKIMKDGIID DFEGAVKQY NYMFDVLKLK PSEQPILVIE STQNEYEKKT ALLKQLLKEN KFVATFLIKN PTCVSFAHGR PNCLVVDLGH D LVTITPIL DGISLRKQVL GTHYAGAFLS QQLRQLLNHK GVEVVPVYKV KSKVPTYFPD EAKFEERKYD FDISESFENF HK LRILREM KETLLQALPD SETEKLKEQE TEEDTRYFEF PNGLNVPFTK YERVRLANSL FNPSEPYTGE SGPNIVVEGF SVE TGKIIN EDTITSREYV PLRRSKKTDS SSGRRSKDEP TDDKPRGLTS LVNQALNHLD VDLKPQLANN IILTGATSLI PGVA ERLNQ ELTAMNPGLK VRIHSSANVI ERTCSAWIGG SILSSLGTFH QLWVSENEYD EVGAKKLIMD RFR

UniProtKB: Actin

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Macromolecule #4: Chromatin modification-related protein EAF1

MacromoleculeName: Chromatin modification-related protein EAF1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii GS115 (fungus) / Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 118.49882 KDa
SequenceString: MSSLDSNVTA SSKHDSPKRQ PEDGSGTNDD PLQRILNERK RKLAELYCVS RLPLLPISPS QVSQIGENLM RFLERNDLEQ GRQFNITTL TGDKSQKQPP VSKEVSTADQ LESPHWPVKE DEETTKDEPP RKKQKTASTS AEPQKATHKE SKMTMMHQEV T ESEAPTLS ...String:
MSSLDSNVTA SSKHDSPKRQ PEDGSGTNDD PLQRILNERK RKLAELYCVS RLPLLPISPS QVSQIGENLM RFLERNDLEQ GRQFNITTL TGDKSQKQPP VSKEVSTADQ LESPHWPVKE DEETTKDEPP RKKQKTASTS AEPQKATHKE SKMTMMHQEV T ESEAPTLS SLIRKYAQDE VPIRPDDPTD RDLNFELLDR NKTIIQALPE IYPHKIADSA SLTELYYLTQ TFPLAKLLPR SH KSLTTDA YESALLEGKI AVLYSRIEEL KRQRKWSLRQ PKRFIDPFTR ESPTHWDHLL AEMKWLSVDI MEERKFKAAS CVQ LAQAVS DYWTYGKIVC IQRKPLIFLT DEEIKERTVT KVMKTEVDNE NEHDHDDNDI FKDAQEEPRA MDQEQNQPFE ENAT IDVAK LLERPNPKDE IIPPALPTYS MGDYKRLNQN AEPFKLHIGL DDFKKEDLVL VEKLPLSFIF DDNLSDSKKK LSEYE KAPI AAISTLLAPP EDDEWYKIVI RRDPASELSA SLDYQKGLFG ASSQRRYNVL KPPKPPPIKN LELRTPTIWL PQDDKL LIR YVAEYAFNWD IISAHLSARP ARAYVANIER RTPWQCFERY IQLNDKFQFT DMRGQYAQSA QAWLEAAHKT QSTTKRR IS PLGVGIESIQ RGHRRLRWGS MLDAMRKCMR RRENINRSSQ VERKHTSDDK RTNVPTPEEL SRLKYDRDKA IQEAYMHQ N SGTFSSARPH TQSSALSPSK GKNAPLPTSA QQTGTHPYTN GIPPKGTLPK TTTPAPGVPS TQPGTPNTRQ PQVSSRVAT SQNTTPVTNR TGTPNGNRPG PNNSFTQEQL QHFLQAQRHR QMMQTSAGTP VNKSNVPNRP AGITNTNVTT PANAVSSSTT PSKSAATAS QQQPSPSRGI NLTPAQVNAL INQIQAQNPN MSKDQVTKFA VAYIQNLQNQ RERSSNGHST PQVRTVPTPT R ATAGPPVS ASPVTSNASP TTPASLTKEK LDALENSPNL TPQQRQQITL FKAMQARNKM NQVANRGQES ASASSNLSAS PN TDTKQTT DTNK

UniProtKB: Chromatin modification-related protein EAF1

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Macromolecule #5: SWR1-complex protein 4

MacromoleculeName: SWR1-complex protein 4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii GS115 (fungus) / Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 64.916418 KDa
SequenceString: MSSDILDVLS ISGRSNLSNQ KKKITKDGPT KKKKQTAMSR ELFNLIGQNT PPLAVEKTVK FKEKLNVNNK PTPWSYVEFS NDARESKDG LKLHHWIKGS SELAKNSPYL FEKYNQKIQI PSFTKEEYDE FLKDLDLECR EREKRDKALK EQEAKEAEKL E KEKENDKE ...String:
MSSDILDVLS ISGRSNLSNQ KKKITKDGPT KKKKQTAMSR ELFNLIGQNT PPLAVEKTVK FKEKLNVNNK PTPWSYVEFS NDARESKDG LKLHHWIKGS SELAKNSPYL FEKYNQKIQI PSFTKEEYDE FLKDLDLECR EREKRDKALK EQEAKEAEKL E KEKENDKE RVNGDELGKE EDNASDFVPK KENVNDQILP KIDEPQTNKK DDMESTEDVS KSDSQEVSKD VNPSEEVEAS WD YDETVHL FQLCEKWDLR WPIIVDRYEY DERSMEELKE RFYKVSERIL RHKYRNVTMD DKTSLLVQTL SSFDKRRETE RKQ YLRRLL SRSPTEIAEE ESLVIEARKF ELAAKKMLTE RASLLRLLDS PQSTGSISQY LTSQGLTQLY NTLMSADRSK RRKV ETPTP PQIPPGASSS LHRTSMDLKR KAAKKIGPNA LLENIKATGN SVPPSGNAPQ SAAIELINTK MTPEEKEAYG IKIHQ EKLQ PGVSLRSARL PTFKPATQAK IVVVLNELEV SPKPTIPTAK VVAQYDNLLQ TINVLLETKK QVNKLEVELN LLEGKE EDK ES

UniProtKB: SWR1-complex protein 4

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Macromolecule #6: Enhancer of polycomb-like protein

MacromoleculeName: Enhancer of polycomb-like protein / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii GS115 (fungus) / Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 86.836922 KDa
SequenceString: MVLPSAAGAR FRQRKISVKQ TLQVFKQSDI ADLETEDQQR ELQKIETGVE KGEEEEEHLQ RVINAAQAAV ISGGKVEKAY IPTPDASQV WKDYDKYYRD KFQPPGTYIR FSATVEETTG CIYNLDEEDE SFLKEVLNKN LANGIKPCTE TELEIVLQRF E VVIDKKQP ...String:
MVLPSAAGAR FRQRKISVKQ TLQVFKQSDI ADLETEDQQR ELQKIETGVE KGEEEEEHLQ RVINAAQAAV ISGGKVEKAY IPTPDASQV WKDYDKYYRD KFQPPGTYIR FSATVEETTG CIYNLDEEDE SFLKEVLNKN LANGIKPCTE TELEIVLQRF E VVIDKKQP FLAMDPSQIL TFEELHSAAL VVDPNSIEEI ELSLEKQLGL HPFRTLLDGQ RSQLSHRKLA ELLRIFGQKI YD HWKQRRI ARHGRPITAQ LRFEDSSEKD DSDPYVCFRR REFRQARKTR RTDTQGSERL RKLHRELKQT RDLLLAVAQR EVK RKEAIE VGHEVFQLRC SVKTLKRDLG VKGEEEDLVA HKRKKVVPTT DEDRKYRKGY NSGNYPNRNQ AQAQQQQQQL QQQQ ISKSG LNPVSIQPYV KLPMSRIPDM DLITVSTVLN EKDEAINRAV AEKLRQRKES DRGWVNLTDD PFNPFLQFTN PDSIL EKGH FPYSSIAAAL FEVDQSNYFD PEITQLIKDK KPLPRTLCFK DNALTTPLPP SIYEVASNNK LDVTAPICKV RKRMGR RGL WIDRKMTVDE PLDEFLDFST FEKSLDADIT DRNSAKSQQG MNVYDSVDDA NSRLRSRFSF DRDVPLFNPV DPSELNQ IS SQTQSIRFGC MLLTKAYEQV HQAKQKLFLE QQQHQQKQQQ KLLQQRQKVQ QKLQQQQQQQ QQAQQQNPKS NTNKVVNQ I NNTKSPVKQS KIPSKVSKNI SGVTTSAGKG A

UniProtKB: Enhancer of polycomb-like protein

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Macromolecule #7: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / 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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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration0.25 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
150.0 mMKOAcPotassium acetate
5.0 mMMgOAcMagnesium acetate
2.0 mMTCEPtris(2-carboxyethyl)phosphine
5.0 mMNH4OAcAmmonium acetate
0.0025 %DDMDodecyl-maltoside
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.8000000000000003 µm / Nominal defocus min: 1.4000000000000001 µm
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 52.8 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1265830
Startup modelType of model: OTHER / Details: cryoSPARC ab-initio reconstruction
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 518386

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