7YFN: Core module of the NuA4 complex in S. cerevisiae

Core module of the NuA4 complex in S. cerevisiae. Determined by electron microscopy at 3.8 Å resolution. Released 8 Mar 2023.

Method
Electron microscopy
Resolution
3.8 Å
Organism
Saccharomyces cerevisiae
Chains
6
Atoms
26,397
Mol. weight
795.34 kDa
Ligands
ATP
Released
8 Mar 2023

Explore 7YFN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7YFN contains 157 α-helices and 80 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 20 helices, 21 β-strands

ElementResiduesLengthSheet
β-strand8-1251
β-strand16-2161
β-strand29-3241
β-strand3612
β-strand3713
β-strand5312
α-helix55-606
β-strand6613
β-strand71-7224
β-strand75-7624
α-helix79-8810
α-helix89-935
α-helix98-1003
β-strand103-10421
β-strand106-10725
α-helix113-12210
α-helix123-1275
β-strand13211
β-strand135-13625
α-helix137-1459
β-strand15016
β-strand153-15537
β-strand160-16237
β-strand16516
β-strand176-17837
α-helix182-19514
α-helix203-21513
α-helix223-23210
β-strand238-24258
β-strand246-25058
α-helix253-26210
α-helix271-2733
α-helix274-28411
α-helix288-2958
β-strand299-30137
α-helix309-32012
α-helix338-34811
α-helix351-3544
α-helix359-3646
α-helix367-3693
α-helix370-3734
Chain B: 17 helices, 20 β-strands
ElementResiduesLengthSheet
β-strand1419
β-strand17-21510
β-strand25-30610
β-strand38-41410
β-strand45-47311
β-strand69-71311
β-strand75-76212
β-strand79-80212
α-helix83-9614
β-strand107-112610
α-helix118-13013
β-strand136-141610
α-helix142-1509
β-strand155-160613
β-strand165-171713
β-strand174-175213
β-strand181-182213
α-helix187-19711
β-strand209-212414
β-strand216-218314
α-helix227-23610
α-helix238-2436
α-helix255-2573
α-helix259-2624
β-strand270-271215
β-strand277-278215
α-helix282-29312
α-helix385-39511
α-helix401-4066
β-strand408-411413
α-helix414-4163
α-helix420-43112
β-strand439-440213
α-helix447-4493
α-helix451-46111
α-helix472-4787
α-helix480-4867
Chain D: 15 helices, 12 β-strands
ElementResiduesLengthSheet
α-helix26-4722
α-helix70-734
β-strand268-270316
β-strand272117
β-strand273-274218
β-strand280-282319
α-helix287-29610
α-helix303-3053
α-helix312-33524
α-helix358-39740
β-strand532120
β-strand533118
β-strand553120
α-helix563-5653
β-strand568-569218
β-strand598-599218
β-strand601-604416
α-helix629-6313
α-helix639-6413
β-strand649-650221
α-helix652-66514
α-helix669-6768
α-helix693-70311
α-helix709-7113
α-helix717-73418
β-strand741-742221
α-helix753-77119
Chain E: 12 helices, 2 β-strands
ElementResiduesLengthSheet
β-strand78-8369
β-strand91-9669
α-helix99-1024
α-helix106-1094
α-helix166-17611
α-helix179-1813
α-helix185-1895
α-helix198-21619
α-helix222-2254
α-helix230-24516
α-helix248-26518
α-helix271-2788
α-helix280-2834
α-helix300-3078
Chain F: 2 helices, 7 β-strands
ElementResiduesLengthSheet
α-helix521-53414
β-strand546-548328
β-strand569-571328
β-strand585117
α-helix616-6172
β-strand618-620319
β-strand631-633316
β-strand636-643818
β-strand647-654818
Chain T: 91 helices, 18 β-strands
ElementResiduesLengthSheet
α-helix837-8459
α-helix856-8649
α-helix880-88910
α-helix894-90411
α-helix913-93119
α-helix939-95113
α-helix971-9733
β-strand977-980422
β-strand982123
β-strand989-992422
α-helix997-10059
α-helix1011-103323
α-helix1039-105113
α-helix1062-10654
α-helix1069-109022
α-helix1096-112429
α-helix1144-115411
α-helix1158-117922
α-helix1182-11876
α-helix1190-120213
α-helix1206-122318
α-helix1229-12324
α-helix1235-124612
α-helix2417-24237
α-helix2429-244214
α-helix2447-245610
α-helix2469-247911
β-strand2480123
α-helix2497-25015
α-helix2505-25073
α-helix2519-253416
α-helix2538-255114
α-helix2553-25619
α-helix2564-25685
α-helix2576-258712
α-helix2604-261310
α-helix2624-26296
α-helix2633-264614
α-helix2653-266917
α-helix2672-268211
α-helix2686-269712
α-helix2700-271314
α-helix2725-274016
α-helix2747-27526
α-helix2755-27606
α-helix2773-278210
α-helix2789-280517
α-helix2813-283018
α-helix2837-286428
α-helix2874-288613
α-helix2896-291621
α-helix2917-29193
α-helix2942-295716
α-helix2960-29678
α-helix2980-299314
α-helix2996-29983
α-helix3019-303214
α-helix3037-305014
α-helix3054-307017
α-helix3079-309113
α-helix3098-310811
α-helix3116-31238
α-helix3130-31367
α-helix3137-31459
α-helix3152-316211
α-helix3164-318118
α-helix3204-321714
α-helix3220-323617
α-helix3241-326121
α-helix3270-32734
α-helix3274-32829
α-helix3289-329911
α-helix3309-332719
β-strand3331-3332224
α-helix3334-33374
α-helix3339-33424
α-helix33521
β-strand3353125
α-helix33541
α-helix3368-33692
β-strand3370125
β-strand3371-3374424
β-strand3378-3382524
β-strand3387-3395924
β-strand3400-3406724
α-helix3413-343220
β-strand3448-3450324
β-strand3456-3458324
β-strand3464-3466326
α-helix3467-347711
α-helix3482-349312
α-helix3494-34985
α-helix3506-352015
α-helix3526-35349
α-helix3538-356023
α-helix3569-35713
β-strand3572-3575426
β-strand3580-3583426
β-strand3590-3591227
β-strand3613-3614227
α-helix3626-36327
α-helix3634-36363
α-helix3637-36415
α-helix3642-365312
α-helix3659-367719
α-helix3686-370621
α-helix3718-372811
α-helix3730-37345
α-helix3738-37403

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
ActinAprotein372Saccharomyces cerevisiaeP60010 (AlphaFold model)
ARP4 isoform 1Bprotein489Saccharomyces cerevisiaeP80428 (AlphaFold model)
Chromatin modification-related protein EAF1Dprotein982Saccharomyces cerevisiaeQ06337 (AlphaFold model)
SWR1-complex protein 4Eprotein476Saccharomyces cerevisiaeP53201 (AlphaFold model)
Transcription-associated protein 1Tprotein3744Saccharomyces cerevisiaeP38811
Enhancer of polycomb-like protein 1Fprotein832Saccharomyces cerevisiaeP43572
Sequence of entity 1 (A), FASTA
>7YFN_1 Actin (chains A)
EVAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGIMVGMGQKDSYVGDEAQSKRG
ILTLRYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPMNPKSNREKMTQIM
FETFNVPAFYVSIQAVLSLYSSGRTTGIVLDSGDGVTHVVPIYAGFSLPHAILRIDLAGR
DLTDYLMKILSERGYSFSTTAEREIVRDIKEKLCYVALDFEQEMQTAAQSSSIEKSYELP
DGQVITIGNERFRAPEALFHPSVLGLESAGIDQTTYNSIMKCDVDVRKELYGNIVMSGGT
TMFPGIAERMQKEITALAPSSMKVKIIAPPERKYSVWIGGSILASLTTFQQMWISKQEYD
ESGPSIVHHKCF
Sequence of entity 2 (B), FASTA
>7YFN_2 ARP4 isoform 1 (chains B)
MSNAALQVYGGDEVSAVVIDPGSYTTNIGYSGSDFPQSILPSVYGKYTADEGNKKIFSEQ
SIGIPRKDYELKPIIENGLVIDWDTAQEQWQWALQNELYLNSNSGIPALLTEPVWNSTEN
RKKSLEVLLEGMQFEACYLAPTSTCVSFAAGRPNCLVVDIGHDTCSVSPIVDGMTLSKST
RRNFIAGKFINHLIKKALEPKEIIPLFAIKQRKPEFIKKTFDYEVDKSLYDYANNRGFFQ
ECKETLCHICPTKTLEETKTELSSTAKRSIESPWNEEIVFDNETRYGFAEELFLPKEDDI
PANWPRSNSGVVKTWRNDYVPLKRTKPSGVNKSDKKVTPTEEKEQEAVSKSTSPAANSAD
TPNETGKRPLEEEKPPKENNELIGLADLVYSSIMSSDVDLRATLAHNVVLTGGTSSIPGL
SDRLMTELNKILPSLKFRILTTGHTIERQYQSWLGGSILTSLGTFHQLWVGKKEYEEVGV
ERLLNDRFR
Sequence of entity 3 (D), FASTA
>7YFN_3 Chromatin modification-related protein EAF1 (chains D)
MSSRPSSAVPNSASLSEDQSSDRSKFPKADDLIDERDRKLTELYCVSRLNQLLELTDENK
LRKEIDAFLKKNDIRRGIRFDEASLPKLLHTAATPITKKKLKDVNLINVPNQRLSDSKMS
RELPENSENVSVKSESHFVPSHDNSIRENMMDSLRPAEKTGGMWNKRPLESTMGGEEERH
EKRQKMQSQSLESSNNSEMASLPISPRPPVPNALAHYTYYENIEYPPADPTEVQPAVKFK
DPLIKNIMAKEIDTSDHYNENNVDALETVFLLMNDYIPSKIPQALPLAELKYMSQTLPLI
NLIPRAHKALTTNIINNALNEARITVVGSRIEELRRLGLWSLRQPKRFIDPWKQHNTHQN
ILLEEAKWMQADFKEGHKYKVAICTAMAQAIKDYWTYGEICCVKRKTLLPGKENKLSDDG
RISEKSGRPSDTSRNDSDISIAGKDDIGIIANVDDITEKESAAANDNDENGKNEAGAKSD
FDFADGLLSQEGAHDQIISSIDTKLLLKKPSSSSEVVLIQHEVAASSALIETEESKKELA
PPFKLSIFVDELNTFEKTLIQDLPLYNGINEERPKKDDSLPFIPISKSVVSLDDNGFYKL
LERQLIDEEPSISQLSKRRGMFYGNRRNHYLRPPAVPSLRYLQNRTPTIWLSEDDQELVK
NINTYGYNWELISAHMTHRLTYSYLSNIERRTPWQCFERFVQLNERFNFSDLKGPRAHSA
QQWLIEAHKFQQRQNRRISPLGVNTESIQRGHRRLRWASMFEAIRKCMKKRENTPRPNPT
QPRKPLDCKNMKVPTPAEMSLLKAQRDEALRRDIQLRRTVKNRLQQRQQQSQQAHSSRAQ
SPIPSNGKSSSNLARNGQASAPRPNQKQYTEQDIIESYSRKLLEQKPDIGPEMALKAAKN
YYRTLREQQQQLKQHQIQQQRQQLQEESSHVQQLQQLQPGSQAPPPKSSPSQSSLSNISN
INSAPRIKSPTPQEILQRFQKQ
Sequence of entity 4 (E), FASTA
>7YFN_4 SWR1-complex protein 4 (chains E)
MSSSDIFDVLNIKQKSRSPTNGQVSVPSSSAANRPKPQVTGMQRELFNLLGENQPPVVIK
SGNNFKEKMLSTSKPSPWSFVEFKANNSVTLRHWVKGSKELIGDTPKESPYSKFNQHLSI
PSFTKEEYEAFMNENEGTQKSVESEKNHNENFTNEKKDESKNSWSFEEIEYLFNLCKKYD
LRWFLIFDRYSYNNSRTLEDLKEKFYYTCRNYFKASDPSNPLLSSLNFSAEKEIERKKYL
QRLLSRSAAEIAEEEALVVESKKFEMAAKRTLAERESLLRLLDSPHSDQTITQYLTSQGM
SQLYNALLADKTRKRKHDLNIPENPWMKQQQQFAQHRQLQQLNVKKSEVKENLSPKKTKR
QRQEMQTALKRKSESAYAEQLLKDFNSDERKALGVITHGEKLSPGVYLRSTKLSTFKPAL
QNKILAILQELSLPSRPVMPSFDVMERQEELLKKINTLIDLKKHVDKYEAGMSITK
Sequence of entity 5 (T), FASTA
>7YFN_5 Transcription-associated protein 1 (chains T)
MSLTEQIEQFASRFRDDDATLQSRYSTLSELYDIMELLNSPEDYHFFLQAVIPLLLNQLK
EVPISYDAHSPEQKLRNSMLDIFNRCLMNQTFQPYAMEVLEFLLSVLPKENEENGILCMK
VLTTLFKSFKSILQDKLDSFIRIIIQIYKNTPNLINQTFYEAGKAEQGDLDSPKEPQADE
LLDEFSKNDEEKDFPSKQSSTEPRFENSTSSNGLRSSMFSFKILSECPITMVTLYSSYKQ
LTSTSLPEFTPLIMNLLNIQIKQQQEAREQAESRGEHFTSISTEIINRPAYCDFILAQIK
ATSFLAYVFIRGYAPEFLQDYVNFVPDLIIRLLQDCPSELSSARKELLHATRHILSTNYK
KLFLPKLDYLFDERILIGNGFTMHETLRPLAYSTVADFIHNIRSELQLSEIEKTIKIYTG
YLLDESLALTVQIMSAKLLLNLVERILKLGKENPQEAPRAKKLLMIIIDSYMNRFKTLNR
QYDTIMKYYGRYETHKKEKAEKLKNSIQDNDKESEEFMRKVLEPSDDDHLMPQPKKEDIN
DSPDVEMTESDKVVKNDVEMFDIKNYAPILLLPTPTNDPIKDAFYLYRTLMSFLKTIIHD
LKVFNPPPNEYTVANPKLWASVSRVFSYEEVIVFKDLFHECIIGLKFFKDHNEKLSPETT
KKHFDISMPSLPVSATKDARELMDYLAFMFMQMDNATFNEIIEQELPFVYERMLEDSGLL
HVAQSFLTSEITSPNFAGILLRFLKGKLKDLGNVDFNTSNVLIRLFKLSFMSVNLFPNIN
EVVLLPHLNDLILNSLKYSTTAEEPLVYFYLIRTLFRSIGGGRFENLYRSIKPILQVLLQ
SLNQMILTARLPHERELYVELCITVPVRLSVLAPYLPFLMKPLVFALQQYPDLVSQGLRT
LELCIDNLTAEYFDPIIEPVIDDVSKALFNLLQPQPFNHAISHNVVRILGKLGGRNRQFL
KPPTDLTEKTELDIDAIADFKINGMPEDVPLSVTPGIQSALNILQSYKSDIHYRKSAYKY
LTCVLLLMTKSSAEFPTNYTELLKTAVNSIKLERIGIEKNFDLEPTVNKRDYSNQENLFL
RLLESVFYATSIKELKDDAMDLLNNLLDHFCLLQVNTTLLNKRNYNGTFNIDLKNPNFML
DSSLILDAIPFALSYYIPEVREVGVLAYKRIYEKSCLIYGEELALSHSFIPELAKQFIHL
CYDETYYNKRGGVLGIKVLIDNVKSSSVFLKKYQYNLANGLLFVLKDTQSEAPSAITDSA
EKLLIDLLSITFADVKEEDLGNKVLENTLTDIVCELSNANPKVRNACQKSLHTISNLTGI
PIVKLMDHSKQFLLSPIFAKPLRALPFTMQIGNVDAITFCLSLPNTFLTFNEELFRLLQE
SIVLADAEDESLSTNIQKTTEYSTSEQLVQLRIACIKLLAIALKNEEFATAQQGNIRIRI
LAVFFKTMLKTSPEIINTTYEALKGSLAENSKLPKELLQNGLKPLLMNLSDHQKLTVPGL
DALSKLLELLIAYFKVEIGRKLLDHLTAWCRVEVLDTLFGQDLAEQMPTKIIVSIINIFH
LLPPQADMFLNDLLLKVMLLERKLRLQLDSPFRTPLARYLNRFHNPVTEYFKKNMTLRQL
VLFMCNIVQRPEAKELAEDFEKELDNFYDFYISNIPKNQVRVVSFFTNMVDLFNTMVITN
GDEWLKKKGNMILKLKDMLNLTLKTIKENSFYIDHLQLNQSIAKFQALYLRFTELSERDQ
NPLLLDFIDFSFSNGIKASYSLKKFIFHNIIASSNKEKQNNFINDATLFVLSDKCLDARI
FVLKNVINSTLIYEVATSGSLKSYLVEDKKPKWLELLHNKIWKNSNAILAYDVLDHHDLF
RFELLQLSAIFIKADPEIIAEIKKDIIKFCWNFIKLEDTLIKQSAYLVTSYFISKFDFPI
KVVTQVFVALLRSSHVEARYLVKQSLDVLTPVLHERMNAAGTPDTWINWVKRVMVENSSS
QNNILYQFLISHPDLFFNSRDLFISNIIHHMNKITFMSNSNSDSHTLAIDLASLILYWEN
KTLEITNVNNTKTDSDGDVVMSDSKSDINPVEADTTAIIVDANNNSPISLHLREACTAFL
IRYVCASNHRAIETELGLRAINILSELISDKHWTNVNVKLVYFEKFLIFQDLDSENILYY
CMNALDVLYVFFKNKTKEWIMENLPTIQNLLEKCIKSDHHDVQEALQKVLQVIMKAIKAQ
GVSVIIEEESPGKTFIQMLTSVITQDLQETSSVTAGVTLAWVLFMNFPDNIVPLLTPLMK
TFSKLCKDHLSISQPKDAMALEEARITTKLLEKVLYILSLKVSLLGDSRRPFLSTVALLI
DHSMDQNFLRKIVNMSRSWIFNTEIFPTVKEKAAILTKMLAFEIRGEPSLSKLFYEIVLK
LFDQEHFNNTEITVRMEQPFLVGTRVEDIGIRKRFMTILDNSLERDIKERLYYVIRDQNW
EFIADYPWLNQALQLLYGSFNREKELSLKNIYCLSPPSILQEYLPENAEMVTEVNDLELS
NFVKGHIASMQGLCRIISSDFIDSLIEIFYQDPKAIHRAWVTLFPQVYKSIPKNEKYGFV
RSIITLLSKPYHTRQISSRTNVINMLLDSISKIESLELPPHLVKYLAISYNAWYQSINIL
ESIQSNTSIDNTKIIEANEDALLELYVNLQEEDMFYGLWRRRAKYTETNIGLSYEQIGLW
DKAQQLYEVAQVKARSGALPYSQSEYALWEDNWIQCAEKLQHWDVLTELAKHEGFTDLLL
ECGWRVADWNSDRDALEQSVKSVMDVPTPRRQMFKTFLALQNFAESRKGDQEVRKLCDEG
IQLSLIKWVSLPIRYTPAHKWLLHGFQQYMEFLEATQIYANLHTTTVQNLDSKAQEIKRI
LQAWRDRLPNTWDDVNMWNDLVTWRQHAFQVINNAYLPLIPALQQSNSNSNINTHAYRGY
HEIAWVINRFAHVARKHNMPDVCISQLARIYTLPNIEIQEAFLKLREQAKCHYQNMNELT
TGLDVISNTNLVYFGTVQKAEFFTLKGMFLSKLRAYEEANQAFATAVQIDLNLAKAWAQW
GFFNDRRLSEEPNNISFASNAISCYLQAAGLYKNSKIRELLCRILWLISIDDASGMLTNA
FDSFRGEIPVWYWITFIPQLLTSLSHKEANMVRHILIRIAKSYPQALHFQLRTTKEDFAV
IQRQTMAVMGDKPDTNDRNGRRQPWEYLQELNNILKTAYPLLALSLESLVAQINDRFKST
TDEDLFRLINVLLIDGTLNYNRLPFPRKNPKLPENTEKNLVKFSTTLLAPYIRPKFNADF
IDNKPDYETYIKRLRYWRRRLENKLDRASKKENLEVLCPHLSNFHHQKFEDIEIPGQYLL
NKDNNVHFIKIARFLPTVDFVRGTHSSYRRLMIRGHDGSVHSFAVQYPAVRHSRREERMF
QLYRLFNKSLSKNVETRRRSIQFNLPIAIPLSPQVRIMNDSVSFTTLHEIHNEFCKKKGF
DPDDIQDFMADKLNAAHDDALPAPDMTILKVEIFNSIQTMFVPSNVLKDHFTSLFTQFED
FWLFRKQFASQYSSFVFMSYMMMINNRTPHKIHVDKTSGNVFTLEMLPSRFPYERVKPLL
KNHDLSLPPDSPIFHNNEPVPFRLTPNIQSLIGDSALEGIFAVNLFTISRALIEPDNELN
TYLALFIRDEIISWFSNLHRPIIENPQLREMVQTNVDLIIRKVAQLGHLNSTPTVTTQFI
LDCIGSAVSPRNLARTDVNFMPWF
Sequence of entity 6 (F), FASTA
>7YFN_6 Enhancer of polycomb-like protein 1 (chains F)
MPTPSNAIEINDGSHKSGRSTRRSGSRSAHDDGLDSFSKGDSGAGASAGSSNSRFRHRKI
SVKQHLKIYLPNDLKHLDKDELQQREVVEIETGVEKNEEKEVHLHRILQMGSGHTKHKDY
IPTPDASMTWNEYDKFYTGSFQETTSYIKFSATVEDCCGTNYNMDERDETFLNEQVNKGS
SDILTEDEFEILCSSFEHAIHERQPFLSMDPESILSFEELKPTLIKSDMADFNLRNQLNH
EINSHKTHFITQFDPVSQMNTRPLIQLIEKFGSKIYDYWRERKIEVNGYEIFPQLKFERP
GEKEEIDPYVCFRRREVRHPRKTRRIDILNSQRLRALHQELKNAKDLALLVAKRENVSLN
WINDELKIFDQRVKIKNLKRSLNISGEDDDLINHKRKRPTIVTVEQREAELRKAELKRAA
AAAAAAKAKNNKRNNQLEDKSSRLTKQQQQQLLQQQQQQQQNALKTENGKQLANASSSST
SQPITSHVYVKLPSSKIPDIVLEDVDALLNSKEKNARKFVQEKMEKRKIEDADVFFNLTD
DPFNPVFDMSLPKNFSTSNVPFASIASSKFQIDRSFYSSHLPEYLKGISDDIRIYDSNGR
SRNKDNYNLDTKRIKKTELYDPFQENLEIHSREYPIKFRKRVGRSNIKYVDRMPNFTTSS
TKSACSLMDFVDFDSIEKEQYSREGSNDTDSINVYDSKYDEFVRLYDKWKYDSPQNEYGI
KFSDEPARLNQISNDTQVIRFGTMLGTKSYEQLREATIKYRRDYITRLKQKHIQHLQQQQ
QQQQQQQQQAQQQKQKSQNNNSNSSNSLKKLNDSLINSEAKQNSSITQKNSS

Ligands and cofactors

IDNameFormulaCopies
ATPAdenosine-5'-triphosphateC10 H16 N5 O13 P31

Primary citation

Structure of the NuA4 histone acetyltransferase complex. Ji, L., Zhao, L., Xu, K. et al. Proc Natl Acad Sci U S A (2022) 119:e2214313119-e2214313119. DOI 10.1073/pnas.2214313119 · PubMed

Other PDB entries of the same protein (UniProt P60010 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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