Structure of the in situ yeast NPC

2024-06-05 REL RCSB RCSB RCSB 2021-06-17 2022-01-26 2022-01-26 2024-06-05 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) DP2 GM123494 United States National Science Foundation (NSF, United States) MRI DBI 1920374 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) P01 GM121203 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01 GM121443 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) P41 GM109824 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01 GM121443 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01 GM45377 United States Structure of the in situ yeast NPC Villa E Singh D NPC, nucleocytoplasmic transport, TRANSLOCASE Akey CW Singh D Ouch C Echeverria I Nudelman I Varberg JM Yu Z Fang F Shi Y Wang J Salzberg D Song K Xu C Gumbart JC Suslov S Unruh J Jaspersen SL Chait BT Sali A Fernandez-Martinez J Ludtke SJ Villa E Rout MP Comprehensive structure and functional adaptations of the yeast nuclear pore complex. Cell 185 361 378.e25 2022 34982960 doi:10.1016/j.cell.2021.12.015 1097-4172 EMD-24224 other EM volume

map of isolated NPC

7n9f FULLOVERLAP yeast NPC yeast NPC 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

Complete yeast NPC from vitrified cells

Saccharomyces cerevisiae 52.0 Nucleoporin NUP170 Saccharomyces cerevisiae 0.169651969 2 LEVO MFQSFFHNNGPAAAGETFSDSRSYPLTNHQEVPRNGLNELASSATKAQQQPTHILNSYPITGSNPLMRASAMGATSGSIN PNMSNMNEHIRVSGMGTSKPLDLAGKYIDHLQHKDSNTPVLDERSYYNSGVDYNFSREKNGLGAFTPFEKQDVFNIPDEI LHEFSTSQTKTDMGIFPELNRCWITIDNKLILWNINNDNEYQVVDDMKHTIQKVALVRPKPNTFVPAVKHLLLISTTMEL FMFAISLDKATNELSVFNTHLSVPVQGIDVIDIVSHERSGRIFFAGQASGLNIWELHYSGSDDWFNSKCSKVCLTKSALL SLLPTNMLSQIPGVDFIQALFEDNSNGNGGFSQETITQLTIDQQRGIIYSLSSKSTIRAYVITEKSLEGPMSIEPAYISR IIGTTTARAAPILGPKYLKIVKISSVAPEENNNLFLVALTVGGVRLYFNGSMGRFNIEALRLESIKFPPSSVTPEVIQQE LLHQQQEQAKRSFPFFSNLMSSEPVLLKFQKKSSVLLETTKASTIISPGIFFSAVIKSSQQTHQQEKKENSSVTGTTATA GSKTVKQQPVTLQHKLFVSVPDYGILKTHGKYVENATFLETAGPVQQIIPLSGLFNATTKPQGFANEFATQYTSETLRVA VLTSTSIEIYKYRTPDEIFEDLIDNPLPFVLNYGAAEACSTALFVTCKSNKSEKLRSNALTFLTMGIPGVVDIKPVYNRY SVSTVSSLLSKPTLSTATTNLQQSITGFSKPSPANKEDFDLDDVILSPRFYGIALLITRLLRDIWGRHVFMTFTDNRVTS HAFISSSDPITPSINNLKSDEISQNRNIISKVSISKDCIEYYLSSINILNEFFITYGDSISQISAPYVLANNSNGRVIDK TEEVANQAESIAINAMIKMVQSIKEGLSFLNVLYEESEVEGFDNQYLGFKDIISFVSLDVQKDLVKLDFKDLFAPNDKTK SLIREILLSIINRNITKGASIEYTATALQERCGSFCSASDILGFRAIEHLRRAKEIGLRNYDSLNYHLKNATALLEQIVD DLSIEKLKEAVSMMLSVNYYPKSIEFLLNIANSMDKGKLACQYVANGFLENDDRKQYYDKRILVYDLVFDTLIKVDELAE KKQSSKTQNQISISNDDEVKLRQKSYEAALKYNDRLFHYHMYDWLVSQNREEKLLDIETPFILPYLMEKAGSSLKISNIL WVYYSRRSKFFESAEILYRLATSNFDITLFERIEFLSRANGFCNSVSPLSQKQRIVQLASRIQDACEVAGIQGDILSLVY TDARIDSAIKDELIKTLDGKILSTSELFNDFAVPLSYHEIALFIFKIADFRDHEVIMAKWDELFQSLRMEFNNTGKKEDS MNFINLLSNVLIKIGKNVQDSEFIFPIFELFPIVCNFFYETLPKEHIVSGSIVSIFITAGVSFNKMYYILKELIETSDSD NSVFNKEMTWLIHEWYKSDRKFRDIISYNDIIHLKEYKIDNDPIEKYVKNSGNNLGICFYKE P38181 Nucleoporin NUP157 Saccharomyces cerevisiae 0.156827484 2 LEVO MYSTPLKKRIDYDRETFTASASLGGNRLRNRPRDDQNNGKPNLSSRSFLSERKTRKDVLNKYGEAGNTIESELRDVTTHV KISGLTSSEPLQLASEFVQDLSFRDRNTPILDNPDYYSKGLDYNFSDEVGGLGAFTPFQRQQVTNIPDEVLSQVSNTEIK SDMGIFLELNYCWITSDNKLILWNINNSSEYHCIDEIEHTILKVKLVKPSPNTFVSSVENLLIVATLFDIYILTISFNDR THELNIFNTGLKVNVTGFNVSNIISYERTGQIFFTGATDGVNVWELQYNCSENLFNSKSNKICLTKSNLANLLPTKLIPS IPGGKLIQKVLEGDAGTEEETISQLEVDQSRGVLHTLSTKSIVRSYLITSNGLVGPVLIDAAHIRRGMNALGVKNSPLLS NRAFKIAKIVSISMCENNDLFLAVITTTGVRLYFKGSISRRSIGSLKLDSVKFPPTSISSSLEQNKSFIIGHHPLNTHDT GPLSTQKASSTYINTTCASTIISPGIYFTCVRKRANSGELSKGITNKALLENKEEHKLYVSAPDYGILKNYGKYVENTAL LDTTDEIKEIVPLTRSFNYTSTPQGYANVFASQYSAEPLKVAVLTSNALEIYCYRTPDEVFESLIENPLPFIHSYGLSEA CSTALYLACKFNKSEHIKSSALAFFSAGIPGVVEIKPKSSRESGSVPPISQNLFDKSGECDGIVLSPRFYGSALLITRLF SQIWEERVFVFKRASKTEKMDAFGISITRPQVEYYLSSISVLADFFNIHRPSFVSFVPPKGSNAITASDAESIAMNALIL LINSIKDALSLINVFYEDIDAFKSLLNTLMGAGGVYDSKTREYFFDLKFHDLFTPNAKTKQLIKEILIEVVNANIASGTS ADYIVNVLKERFGSFCHSADILCYRAGEHLEAAQKFEMIDSKISRNHLDTAIDLYERCAENIELCELRRVVDIMVKLNYQ PKTVGFLLRFADKIDKGNQAQEYVSRGCNTADPRKVFYDKRINVYTLIFEIVKSVDDYTSIEQSPSIANISIFSPASSLK KRVYSVIMNSNNRFFHYCFYDWLVANKRQDYLLRLDSQFVLPYLKERAEKSLEISNLLWFYLFKEEHFLEAADVLYALAS SDFDLKLSERIECLARANGLCDSSTSFDQKPALVQLSENIHELFDIASIQDDLLNLVRNETRIDEDYRKQLTLKLNGRVL PLSDLFNDCADPLDYYEIKLRIFKVSQFKDEKVIQGEWNRLLDSMKNAPSPDVGSVGQESFLSSISNTLIRIGKTTRDTD VVFPVHFLMNKILESFIDKSSAADGSVCSMFLLAGVSHLKLYYILSRIIENSEGNVELAKKEMVWLIKDWYQSDSDLRGS IAPEQIKKLEKYDPNTDPVQDYVKDRHHGLK P40064 orphans bound to Nup192 NTD Saccharomyces cerevisiae 0.0030817899999999996 2 LEVO (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) Nucleoporin NSP1 Saccharomyces cerevisiae 0.086611672 6 LEVO MNFNTPQQNKTPFSFGTANNNSNTTNQNSSTGAGAFGTGQSTFGFNNSAPNNTNNANSSITPAFGSNNTGNTAFGNSNPT SNVFGSNNSTTNTFGSNSAGTSLFGSSSAQQTKSNGTAGGNTFGSSSLFNNSTNSNTTKPAFGGLNFGGGNNTTPSSTGN ANTSNNLFGATANANKPAFSFGATTNDDKKTEPDKPAFSFNSSVGNKTDAQAPTTGFSFGSQLGGNKTVNEAAKPSLSFG SGSAGANPAGASQPEPTTNEPAKPALSFGTATSDNKTTNTTPSFSFGAKSDENKAGATSKPAFSFGAKPEEKKDDNSSKP AFSFGAKSNEDKQDGTAKPAFSFGAKPAEKNNNETSKPAFSFGAKSDEKKDGDASKPAFSFGAKPDENKASATSKPAFSF GAKPEEKKDDNSSKPAFSFGAKSNEDKQDGTAKPAFSFGAKPAEKNNNETSKPAFSFGAKSDEKKDGDASKPAFSFGAKS DEKKDSDSSKPAFSFGTKSNEKKDSGSSKPAFSFGAKPDEKKNDEVSKPAFSFGAKANEKKESDESKSAFSFGSKPTGKE EGDGAKAAISFGAKPEEQKSSDTSKPAFTFGAQKDNEKKTEESSTGKSTADVKSSDSLKLNSKPVELKPVSLDNKTLDDL VTKWTNQLTESASHFEQYTKKINSWDQVLVKGGEQISQLYSDAVMAEHSQNKIDQSLQYIERQQDELENFLDNFETKTEA LLSDVVSTSSGAAANNNDQKRQQAYKTAQTLDENLNSLSSNLSSLIVEINNVSNTFNKTTNIDINNEDENIQLIKILNSH FDALRSLDDNSTSLEKQINSIKK P14907 Nucleoporin NUP57 Saccharomyces cerevisiae 0.057547144999999994 4 LEVO MFGFSGSNNGFGNKPAGSTGFSFGQNNNNTNTQPSASGFGFGGSQPNSGTATTGGFGANQATNTFGSNQQSSTGGGLFGN KPALGSLGSSSTTASGTTATGTGLFGQQTAQPQQSTIGGGLFGNKPTTTTGGLFGNSAQNNSTTSGGLFGNKVGSTGSLM GGNSTQNTSNMNAGGLFGAKPQNTTATTGGLFGSKPQGSTTNGGLFGSGTQNNNTLGGGGLFGQSQQPQTNTAPGLGNTV STQPSFAWSKPSTGSNLQQQQQQQIQVPLQQTQAIAQQQQLSNYPQQIQEQVLKCKESWDPNTTKTKLRAFVYNKVNETE AILYTKPGHVLQEEWDQAMEKKPSPQTIPIQIYGFEGLNQRNQVQTENVAQARIILNHILEKSTQLQQKHELDTASRILK AQSRNVEIEKRILKLGTQLATLKNRGLPLGIAEEKMWSQFQTLLQRSEDPAGLGKTNELWARLAILKERAKNISSQLDSK LMVFNDDTKNQDSMSKGTGEESNDRINKIVEILTNQQRGITYLNEVLEKDAAIVKKYKNKT P48837 Nucleoporin NUP49/NSP49 Saccharomyces cerevisiae 0.049174762 4 LEVO MFGLNKASSTPAGGLFGQASGASTGNANTGFSFGGTQTGQNTGPSTGGLFGAKPAGSTGGLGASFGQQQQQSQTNAFGGS ATTGGGLFGNKPNNTANTGGGLFGANSNSNSGSLFGSNNAQTSRGLFGNNNTNNINNSSSGMNNASAGLFGSKPAGGTSL FGNTSTSSAPAQNQGMFGAKPAGTSLFGNNAGNTTTGGGLFGSKPTGATSLFGSSNNNNNNNNSNNIMSASGGLFGNQQQ QLQQQPQMQCALQNLSQLPITPMTRISELPPQIRQEIEQLDQYIQKQVQISHHLKADTIDHDELIDSIPRDVAYLLKSES ATSQYLKQDLKKISSFKSLIDEDLLDTQTFSVLLQQLLTPGSKISSNDLDKFFQKKIHLYEKKLEDYCRILSDIETAVNG IDTDLFGAPNNPNSTAITADLGSSEAENLLQLKTGLAAIVSTVIEEFTLFMDIAERIAVLHQKTKTLASLSI Q02199 Nucleoporin NUP192 Saccharomyces cerevisiae 0.191718125 2 LEVO MKWSAIPFQTLYRSIESGEFDFDLFKEVLPDLQNLNLNTDKLKNNASRSQLEKGEIELSDGSTFKVNQEFIFEAISLSDE LNLDEIVACELILSGDTTANNGKVQYFLRRQYILQIVSFIVNCFHEDTELYQELIKNGALVSNILSAFKFIHTQLSEIKQ QINKAQILENYNALFQQNIKFRRDFLLREYDILSQILYGLVDKGAIMKNKDFILSLLHHVSELDSNDFFIIYYTPAFFHL FASLRVLPDADVKLLHSQFMKDLKDDSIYTKPVKVALIFIFFAYFIGWCKEDPKRRADTMDFKTDVDEPMTSAVELGAIE QILIFAADTSIVEQDKSMELFYDIRSLLERHIPRLIPKQLLDDEKIFSQTTNSTYNPASATDNMSGRGLWNPSYPGMMST TGTARLNSMPNNVNEYSYTTIVLSDQTQEFFLSSFDDVLQTIITDCAFLLTKIKDAEEDSLLSGEDLTLDDISLKADLER FFLSIYFFYASRPEYSCTFWSDKESNAYGFIEWCSRCNDNLMRSCFYLMVSSLSFGPENALNVYHYFGENSSISWKNIAQ CLSDYTKKISNFNSSLHKRQQFSESTHNDIDSTAVALEEGLNEEAVIFLSSLLTLVGSVTYQVDEDVKSSLSKVFSDVLF EFTKINTPLVGAAFKVISNLVPKLESSRTKFWSFLDSLIFKDSSLNYSSESYRNAFTNVLTKYSDVLGFLQLFHNLISIH SRENNSEYMVFGKLAFPTRLGQGYRKVGIWPYFDYIFNDILAHVDQIVDIRNKRAVQLPILKIIYTGLCSFDYSVILNSI PAAANLDALVDCENFFNYVQECPAIPIFNYIFTEKIYKSIFNVVDVGVDQLSIELEGGKNQAELLQLAVKIINKVLDYQE TYVEELFPIVKKHGKTDYFLPKNYSLHGLRSFYDAIFFNIPLVAHLGLYVGVDDQILATNSLRILAKLSERSNGSVASLS KRNKLLTIFDSVDESARIKDAFITQLESSITDAGVLALKLELLDFLTSNLSNYSRTMTISHLLLGFQVSNVISLGPNLAT FISSGTSLLDSLISVLEASLNSITKDNIDYAPMRLATAALEIILKLCRNPLTSGLLYSYLIKENFFERIMILDPQVTRFT TWNGSPFDNSTEEKCKNFIESESVGAFLSFLAYRNYWTQYLGLFIHKISFSGTKSEVLTYVNYLISNTMYSVRLFSFLDP LNYGNICEPKETLSIFTNVPLNLEQVTLNKYCSGNIYDFHKMENLMRLIKRVRAESLHSNSFSLTVSKEQFLKDADVECI KAKSHFTNIISRNKALELNLSVLHSWVQLVQIIVTDGKLEPSTRSNFILEVFGTIIPKISDYIEFNITFSEELVSLAVFL FDIYNRDRKLITDKGTVDGRLYQLFKTCIQGINSPLSSVALRSDFYILANHYLSRVLSDQVGSEKVLQDLRLGSKKLVEI IWNDVVYGEGTSRVTGILLLDSLIQLANRSKENFILDSLMKTTRLLLIIRSLKNTDALLNSTTEHINIDDLLYELTAFKA TVFFLIRVAETRGGASALIENNLFRIIAELSFLKVDPDLGLDLMFDEVYVQNSKFLKVNVTLDNPLLVDKDANGVSLFEL IVPIFQLISAVLVSMGSSNKAVVQTVKGLLNTYKRLVIGIFKRDLLREKEDKKNSSDPNNQSLNEMVKLIVMLCTLTGYQ NND P47054 Nucleoporin NUP188 Saccharomyces cerevisiae 0.18875328099999997 2 LEVO MATPSFGNSSPQLTFTHVANFMNDAAADVSAVDAKQLAQIRQFLKANKTNLIESLNTIRQNVTSSGDHNKLRSTIANLLQ INVDNDPFFAQSEDLSHAVEFFMSERSSRLHIVYSLLVNPDIDLETYSFIDNDRFNVVGKLISIISSVIQNYDIITASSL AHDYNNDQDMFTIVSLVQLKKFSDLKFILQILQILNLMILNTKVPVDIVNQWFLQYQNQFVEFCRNINSTDKSIDTSSLQ LYKFQNFQDLSYLSETLISRISSLFTITTILILGLNTSIAQFDIQSPLYMDTETFDTVNSALENDVATNIVNEDPIFHPM IHYSWSFILYYRRALQSSESFDDSDITKFALFAESHDVLQKLNTLSEILSFDPVYTTVITVFLEFSLNFIPITASTSRVF AKIISKAPEQFIENFLTNDTFEKKLSIIKAKLPLLNESLIPLINLALIDTEFANFELKDICSFAVTKSSLNDLDYDLIAD TITNSSSSSDIIVPDLIELKSDLLVAPPLENENSNCLLSIPKSTKGKILTIKQQQQQQQQQNGQQPPTTSNLIIFLYKFN GWSLVGRILQNLLHSYMEKGTQLDDLQHELMISIIKLVTNVVDPKTSIEKSSEILSYLSNSLDTSASTINGASIIQVIFE IFEISLQRKDYTSIVQCCEFMTMLTPNYLHLVSSYLNKSDLLDKYGKTGLSNMILGSVELSTGDYTFTIQLLKLTKVFIR ESLSLKNIHISKRSKIDIINKLILHAIHIFESYYNWKYNNFLQKFEIAFHLTLIFYDVLHDVFTINPHQKDQLIISSSAN KLLQLFLTPMDSIDLAPNTLTNILISPLNTTTKILGDKILGNLYSKVMNNSFKLCTLLIAIRGSNRDLKPSNLEKLLFIN SSKLVDVYTLPSYVHFKVQIIELLSYLVEAPWNDDYPFLLSFLGEAKSMAFLKEVLSDLSSPVQDWNLLRSLYIFFTTLL ESKQDGLSILFLTGQFASNKKINDESSIDKKSSILTVLQKNSLLLDSTPEEVSCKLLETITYVLNTWTNSKIFIKDPKFV NSLLAKLKDSKKLFQKKENLTRDETVSLIKKYKLISRIVEIFALCIYNSTDSNSEILNFLNQEDLFELVHHFFQIDGFNK TFHDELNLKFKEKWPSLELQSFQKIPLSRINENENFGYDIPLLDIVLKADRSWNEPSKSQTNFKEEITDASLNLQYVNYE ISTAKAWGALITTFVKRSTVPLNDGFVDLVEHFLKLNIDFGSDKQMFTQIYLERIELSFYILYSFKLSGKLLKEEKIIEL MNKIFTIFKSGEIDFIKNIGKSLKNNFYRPLLRSVLVLLELVSSGDRFIELISDQLLEFFELVFSKGVYLILSEILCQIN KCSTRGLSTDHTTQIVNLEDNTQDLLLLLSLFKKITNVNPSKNFNVILASSLNEVGTLKVILNLYSSAHLIRINDEPILG QITLTFISELCSIEPIAAKLINSGLYSVLLESPLSVAIQQGDIKPEFSPRLHNIWSNGLLSIVLLLLSQFGIKVLPETCL FVSYFGKQIKSTIYNWGDNKLAVSSSLIKETNQLVLLQKMLNLLNYQELFIQPKNSDDQQEAVELVIGLDSEHDKKRLSA ALSKFLTHPKYLNSRIIPTTLEEQQQLEDESSRLEFVKGISRDIKALQDSLFKDV P52593 Nucleoporin NIC96 Saccharomyces cerevisiae 0.09629158599999998 4 LEVO MLETLRGNKLHSGTSKGANKKLNELLESSDNLPSASSELGSIQVSINELRRRVFQLRSKNKASKDYTKAHYLLANSGLSF EDVDAFIKDLQTNQFLEPNPPKIIESEELEFYIRTKKEENILMSIEQLLNGATKDFDNFINHNLNLDWAQHKNEVMKNFG ILIQDKKTVDHKKSISSLDPKLPSWGNKGNNILNSNESRLNVNENNILREKFENYARIVFQFNNSRQANGNFDIANEFIS ILSSANGTRNAQLLESWKILESMKSKDINIVEVGKQYLEQQFLQYTDNLYKKNMNEGLATNVNKIKSFIDTKLKKADKSW KISNLTVINGVPIWALIFYLLRAGLIKEALQVLVENKANIKKVEQSFLTYFKAYASSKDHGLPVEYSTKLHTEYNQHIKS SLDGDPYRLAVYKLIGRCDLSRKNIPAVTLSIEDWLWMHLMLIKEKDAENDPVYERYSLEDFQNIIISYGPSRFSNYYLQ TLLLSGLYGLAIDYTYTFSEMDAVHLAIGLASLKLFKIDSSTRLTKKPKRDIRFANILANYTKSFRYSDPRVAVEYLVLI TLNEGPTDVELCHEALRELVLETKEFTVLLGKIGRDGARIPGVIEERQPLLHVRDEKEFLHTITEQAARRADEDGRIYDS ILLYQLAEEYDIVITLVNSLLSDTLSASDLDQPLVGPDDNSETNPVLLARRMASIYFDNAGISRQIHVKNKEICMLLLNI SSIRELYFNKQWQETLSQMELLDLLPFSDELSARKKAQDFSNLDDNIVKNIPNLLIITLSCISNMIHILNESKYQSSTKG QQIDSLKNVARQCMIYAGMIQYRMPRETYSTLINIDVSL P34077 Nucleoporin NUP53 Saccharomyces cerevisiae 0.052688667999999994 2 LEVO MADLQKQENSSRFTNVSVIAPESQGQHEQQKQQEQLEQQKQPTGLLKGLNGFPSAPQPLFMEDPPSTVSGELNDNPAWFN NPRKRAIPNSIIKRSNGQSLSPVRSDSADVPAFSNSNGFNNVTFGSKKDPRILKNVSPNDNNSANNNAHSSDLGTVVFDS NEAPPKTSLADWQKEDGIFSSKTDNIEDPNLSSNITFDGKPTATPSPFRPLEKTSRILNFFDKNTKTTPNTASSEASAGS KEGASTNWDDHAIIIFGYPETIANSIILHFANFGEILEDFRVIKDFKKLNSKNMSKSPSLTAQKYPIYTGDGWVKLTYKS ELSKSRALQENGIIMNGTLIGCVSYSPAALKQLASLKKSEEIINNKTSSQTSLSSKDLSNYRKTEGIFEKAKAKAVTSKV RNAEFKVSKNSTSFKNPRRLEIKDGRSLFLRNRGKIHSGVLSSIESDLKKREQASKSKKSWLNRLNNWLFGWNDL Q03790 Nucleoporin ASM4 Saccharomyces cerevisiae 0.058853902 2 LEVO MFGIRSGNNNGGFTNLTSQAPQTTQMFQSQSQLQPQPQPQPQQQQQHLQFNGSSDASSLRFGNSLSNTVNANNYSSNIGN NSINNNNIKNGTNNISQHGQGNNPSWVNNPKKRFTPHTVIRRKTTKQNSSSDINQNDDSSSMNATMRNFSKQNQDSKHNE RNKSAANNDINSLLSNFNDIPPSVTLQDWQREDEFGSIPSLTTQFVTDKYTAKKTNRSAYDSKNTPNVFDKDSYVRIANI EQNHLDNNYNTAETNNKVHETSSKSSSLSAIIVFGYPESISNELIEHFSHFGHIMEDFQVLRLGRGINPNTFRIFHNHDT GCDENDSTVNKSITLKGRNNESNNKKYPIFTGESWVKLTYNSPSSALRALQENGTIFRGSLIGCIPYSKNAVEQLAGCKI DNVDDIGEFNVSMYQNSSTSSTSNTPSPPNVIITDGTLLREDDNTPAGHAGNPTNISSPIVANSPNKRLDVIDGKLPFMQ NAGPNSNIPNLLRNLESKMRQQEAKYRNNEPAGFTHKLSNWLFGWNDL Q05166 Nucleoporin NUP82 Saccharomyces cerevisiae 0.082174047 2 LEVO MSQSSRLSALPIFQASLSASQSPRYIFSSQNGTRIVFIQDNIIRWYNVLTDSLYHSLNFSRHLVLDDTFHVISSTSGDLL CLFNDNEIFVMEVPWGYSNVEDVSIQDAFQIFHYSIDEEEVGPKSSIKKVLFHPKSYRDSCIVVLKEDDTITMFDILNSQ EKPIVLNKPNNSFGLDARVNDITDLEFSKDGLTLYCLNTTEGGDIFAFYPFLPSVLLLNEKDLNLILNKSLVMYESLDST TDVIVKRNVIKQLQFVSKLHENWNSRFGKVDIQKEYRLAKVQGPFTINPFPGELYDYTATNIATILIDNGQNEIVCVSFD DGSLILLFKDLEMSMSWDVDNYVYNNSLVLIERVKLQREIKSLITLPEQLGKLYVISDNIIQQVNFMSWASTLSKCINES DLNPLAGLKFESKLEDIATIERIPNLAYINWNDQSNLALMSNKTLTFQNISSDMKPQSTAAETSISTEKSDTVGDGFKMS FTQPINEILILNDNFQKACISPCERIIPSADRQIPLKNEASENQLEIFTDISKEFLQRIVKAQTLGVSIHNRIHEQQFEL TRQLQSTCKIISKDDDLRRKFEAQNKKWDAQLSRQSELMERFSKLSKKLSQIAESNKFKEKKISHGEMKWFKEIRNQILQ FNSFVHSQKSLQQDLSYLKSELTRIEAETIKVDKKSQNEWDELRKMLEIDSKIIKECNEELLQVSQEFTTKTQ P40368 Nucleoporin NUP159 Saccharomyces cerevisiae 0.159067188 2 LEVO MSSLKDEVPTETSEDFGFKFLGQKQILPSFNEKLPFASLQNLDISNSKSLFVAASGSKAVVGELQLLRDHITSDSTPLTF KWEKEIPDVIFVCFHGDQVLVSTRNALYSLDLEELSEFRTVTSFEKPVFQLKNVNNTLVILNSVNDLSALDLRTKSTKQL AQNVTSFDVTNSQLAVLLKDRSFQSFAWRNGEMEKQFEFSLPSELEELPVEEYSPLSVTILSPQDFLAVFGNVISETDDE VSYDQKMYIIKHIDGSASFQETFDITPPFGQIVRFPYMYKVTLSGLIEPDANVNVLASSCSSEVSIWDSKQVIEPSQDSE RAVLPISEETDKDTNPIGVAVDVVTSGTILEPCSGVDTIERLPLVYILNNEGSLQIVGLFHVAAIKSGHYSINLESLEHE KSLSPTSEKIPIAGQEQEEKKKNNESSKALSENPFTSANTSGFTFLKTQPAAANSLQSQSSSTFGAPSFGSSAFKIDLPS VSSTSTGVASSEQDATDPASAKPVFGKPAFGAIAKEPSTSEYAFGKPSFGAPSFGSGKSSVESPASGSAFGKPSFGTPSF GSGNSSVEPPASGSAFGKPSFGTPSFGSGNSSAEPPASGSAFGKPSFGTSAFGTASSNETNSGSIFGKAAFGSSSFAPAN NELFGSNFTISKPTVDSPKEVDSTSPFPSSGDQSEDESKSDVDSSSTPFGTKPNTSTKPKTNAFDFGSSSFGSGFSKALE SVGSDTTFKFGTQASPFSSQLGNKSPFSSFTKDDTENGSLSKGSTSEINDDNEEHESNGPNVSGNDLTDSTVEQTSSTRL PETPSDEDGEVVEEEAQKSPIGKLTETIKKSANIDMAGLKNPVFGNHVKAKSESPFSAFATNITKPSSTTPAFSFGNSTM NKSNTSTVSPMEEADTKETSEKGPITLKSVENPFLPAKEERTGESSKKDHNDDPKDGYVSGSEISVRTSESAFDTTANEE IPKSQDVNNHEKSETDPKYSQHAVVDHDNKSKEMNETSKNNERSGQPNHGVQGDGIALKKDNEKENFDSNMAIKQFEDHQ SSEEDASEKDSRQSSEVKESDDNMSLNSDRDESISESYDKLEDINTDELPHGGEAFKAREVSASADFDVQTSLEDNYAES GIQTDLSESSKENEVQTDAIPVKHNSTQTVKKEAVDNGLQTEPVETCNFSVQTFEGDENYLAEQCKPKQLKEYYTSAKVS NIPFVSQNSTLRLIESTFQTVEAEFTVLMENIRNMDTFFTDQSSIPLVKRTVRSINNLYTWRIPEAEILLNIQNNIKCEQ MQITNANIQDLKEKVTDYVRKDIAQITEDVANAKEEYLFLMHFDDASSGYVKDLSTHQFRMQKTLRQKLFDVSAKINHTE ELLNILKLFTVKNKRLDDNPLVAKLAKESLARDGLLKEIKLLREQVSRLQLEEKGKKASSFDASSSITKDMKGFKVVEVG LAMNTKKQIGDFFKNLNMAK P40477 Nucleoporin NUP120 Saccharomyces cerevisiae 0.120560328 2 LEVO MACLSRIDANLLQYYEKPEPNNTVDLYVSNNSNNNGLKEGDKSISTPVPQPYGSEYSNCLLLSNSEYICYHFSSRSTLLT FYPLSDAYHGKTINIHLPNASMNQRYTLTIQEVEQQLLVNVILKDGSFLTLQLPLSFLFSSANTLNGEWFHLQNPYDFTV RVPHFLFYVSPQFSVVFLEDGGLLGLKKVDGVHYEPLLFNDNSYLKSLTRFFSRSSKSDYDSVISCKLFHERYLIVLTQN CHLKIWDLTSFTLIQDYDMVSQSDSDPSHFRKVEAVGEYLSLYNNTLVTLLPLENGLFQMGTLLVDSSGILTYTFQNNIP TNLSASAIWSIVDLVLTRPLELNVEASYLNLIVLWKSGTASKLQILNVNDESFKNYEWIESVNKSLVDLQSEHDLDIVTK TGDVERGFCNLKSRYGTQIFERAQQILSENKIIMAHNEDEEYLANLETILRDVKTAFNEASSITLYGDEIILVNCFQPYN HSLYKLNTTVENWFYNMHSETDGSELFKYLRTLNGFASTLSNDVLRSISKKFLDIITGELPDSMTTVEKFTDIFKNCLEN QFEITNLKILFDELNSFDIPVVLNDLINNQMKPGIFWKKDFISAIKFDGFTSIISLESLHQLLSIHYRITLQVLLTFVLF DLDTEIFGQHISTLLDLHYKQFLLLNLYRQDKCLLAEVLLKDSSEFSFGVKFFNYGQLIAYIDSLNSNVYNASITENSFF MTFFRSYIIENTSHKNIRFFLENVECPFYLRHNEVQEFMFAMTLFSCGNFDQSYEIFQLHDYPEAINDKLPTFLEDLKSE NYHGDSIWKDLLCTFTVPYRHSAFYYQLSLLFDRNNSQEFALKCISKSAEYSLKEIQIEELQDFKEKQHIHYLNLLIHFR MFEEVLDVLRLGHECLSDTVRTNFLQLLLQEDIYSRDFFSTLLRLCNAHSDNGELYLRTVDIKIVDSILSQNLRSGDWEC FKKLYCFRMLNKSERAAAEVLYQYILMQADLDVIRKRKCYLMVINVLSSFDSAYDQWILNGSKVVTLTDLRDELRGL P35729 Nucleoporin NUP85 Saccharomyces cerevisiae 0.084972438 2 LEVO MTIDDSNRLLMDVDQFDFLDDGTAQLSNNKTDEEEQLYKRDPVSGAILVPMTVNDQPIEKNGDKMPLKFKLGPLSYQNMA FITAKDKYKLYPVRIPRLDTSKEFSAYVSGLFEIYRDLGDDRVFNVPTIGVVNSNFAKEHNATVNLAMEAILNELEVFIG RVKDQDGRVNRFYELEESLTVLNCLRTMYFILDGQDVEENRSEFIESLLNWINRSDGEPDEEYIEQVFSVKDSTAGKKVF ETQYFWKLLNQLVLRGLLSQAIGCIERSDLLPYLSDTCAVSFDAVSDSIELLKQYPKDSSSTFREWKNLVLKLSQAFGSS ATDISGELRDYIEDFLLVIGGNQRKILQYSRTWYESFCGFLLYYIPSLELSAEYLQMSLEANVVDITNDWEQPCVDIISG KIHSILPVMESLDSCTAAFTAMICEAKGLIENIFEGEKNSDDYSNEDNEMLEDLFSYRNGMASYMLNSFAFELCSLGDKE LWPVAIGLIALSATGTRSAKKMVIAELLPHYPFVTNDDIEWMLSICVEWRLPEIAKEIYTTLGNQMLSAHNIIESIANFS RAGKYELVKSYSWLLFEASCMEGQKLDDPVLNAIVSKNSPAEDDVIIPQDILDCVVTNSMRQTLAPYAVLSQFYELRDRE DWGQALRLLLLLIEFPYLPKHYLVLLVAKFLYPIFLLDDKKLMDEDSVATVIEVIETKWDDADEKSSNLYETIIEADKSL PSSMATLLKNLRKKLNFKLCQAFM P46673 Nucleoporin 145c Saccharomyces cerevisiae 0.08115785199999999 2 LEVO SIWGLVNEEDAEIDEDDLSKQEDGGEQPLRKVRTLAQSKPSDKEVILKTDGTFGTLSGKDDSIVEEKAYEPDLSDADFEG IEASPKLDVSKDWVEQLILAGSSLRSVFATSKEFDGPCQNEIDLLFSECNDEIDNAKLIMKERRFTASYTFAKFSTGSML LTKDIVGKSGVSIKRLPTELQRKFLFDDVYLDKEIEKVTIEARKSNPYPQISESSLLFKDALDYMEKTSSDYNLWKLSSI LFDPVSYPYKTDNDQVKMALLKKERHCRLTSWIVSQIGPEIEEKIRNSSNEIEQIFLYLLLNDVVRASKLAIESKNGHLS VLISYLGSNDPRIRDLAELQLQKWSTGGCSIDKNISKIYKLLSGSPFEGLFSLKELESEFSWLCLLNLTLCYGQIDEYSL ESLVQSHLDKFSLPYDDPIGVIFQLYAANENTEKLYKEVRQRTNALDVQFCWYLIQTLRFNGTRVFSKETSDEATFAFAA QLEFAQLHGHSLFVSCFLNDDKAAEDTIKRLVMREITLLRASTNDHILNRLKIPSQLIFNAQALKDRYEGNYLSEVQNLL LGSSYDLAEMAIVTSLGPRLLLSNNPVQNNELKTLREILNEFPDSERDKWSVSINVFEVYLKLVLDNVETQETIDSLISG MKIFYDQYKHCREVAACCNVMSQEIVSKILEKNNPSIGDSKAKLLELPLGQPEKAYLRGEFAQDLMKCTYKI P49687 Protein transport protein SEC13 Saccharomyces cerevisiae 0.03308296499999999 2 LEVO MVVIANAHNELIHDAVLDYYGKRLATCSSDKTIKIFEVEGETHKLIDTLTGHEGPVWRVDWAHPKFGTILASCSYDGKVL IWKEENGRWSQIAVHAVHSASVNSVQWAPHEYGPLLLVASSDGKVSVVEFKENGTTSPIIIDAHAIGVNSASWAPATIEE DGEHNGTKESRKFVTGGADNLVKIWKYNSDAQTYVLESTLEGHSDWVRDVAWSPTVLLRSYLASVSQDRTCIIWTQDNEQ GPWKKTLLKEEKFPDVLWRASWSLSGNVLALSGGDNKVTLWKENLEGKWEPAGEVHQ Q04491 Nucleoporin SEH1 Saccharomyces cerevisiae 0.039170758 2 LEVO MQPFDSGHDDLVHDVVYDFYGRHVATCSSDQHIKVFKLDKDTSNWELSDSWRAHDSSIVAIDWASPEYGRIIASASYDKT VKLWEEDPDQEECSGRRWNKLCTLNDSKGSLYSVKFAPAHLGLKLACLGNDGILRLYDALEPSDLRSWTLTSEMKVLSIP PANHLQSDFCLSWCPSRFSPEKLAVSALEQAIIYQRGKDGKLHVAAKLPGHKSLIRSISWAPSIGRWYQLIATGCKDGRI RIFKITEKLSPLASEESLTNSNMFDNSADVDMDAQGRSDSNTEEKAELQSNLQVELLSEHDDHNGEVWSVSWNLTGTILS SAGDDGKVRLWKATYSNEFKCMSVITAQQ P53011 Nucleoporin NUP84 Saccharomyces cerevisiae 0.08371886699999999 2 LEVO MELSPTYQTERFTKFSDTLKEFKIEQNNEQNPIDPFNIIREFRSAAGQLALDLANSGDESNVISSKDWELEARFWHLVEL LLVFRNADLDLDEMELHPYNSRGLFEKKLMQDNKQLYQIWIVMVWLKENTYVMERPKNVPTSKWLNSITSGGLKSCDLDF PLRENTNVLDVKDKEEDHIFFKYIYELILAGAIDEALEEAKLSDNISICMILCGIQEYLNPVIDTQIANEFNTQQGIKKH SLWRRTVYSLSQQAGLDPYERAIYSYLSGAIPNQEVLQYSDWESDLHIHLNQILQTEIENYLLENNQVGTDELILPLPSH ALTVQEVLNRVASRHPSESEHPIRVLMASVILDSLPSVIHSSVEMLLDVVKGTEASNDIIDKPYLLRIVTHLAICLDIIN PGSVEEVDKSKLITTYISLLKLQGLYENIPIYATFLNESDCLEACSFILSSLEDPQVRKKQIETINFLRLPASNILRRTT QRVFDETEQEYSPSNEISISFDVNNIDMHLIYGVEWLIEGKLYVDAVHSIIALSRRFLLNGRVKALEQFMERNNIGEICK NYELEKIADNISKDENEDQFLEEITQYEHLIKGIREYEEWQKSVSLLSSESNIPTLIEKLQGFSKDTFELIKTFLVDLTS SNFADSADYEILYEIRALYTPFLLMELHKKLVEAAKLLKIPKFISEALAFTSLVANENDKIYLLFQSSGKLKEYLDLVAR TATLSN P52891 Nucleoporin NUP133 Saccharomyces cerevisiae 0.133452672 2 LEVO MSEKKVHLRLRKELSVPIAVVENESLAQLSYEEESQASLMDISMEQQQLRLHSHFDNSKVFTENNRYIVKTLQTDYSSGF SNDDELNGYIDMQIGYGLVNDHKKVYIWNIHSTQKDTPYITVPFRSDDNDEIAVAPRCILTFPATMDESPLALNPNDQDE TGGLIIIKGSKAIYYEDINSINNLNFKLSEKFSHELELPINSSGGEKCDLMLNCEPAGIVLSTNMGRIFFITIRNSMGKP QLKLGKLLNKPFKLGIWSKIFNTNSSVVSLRNGPILGKGTRLVYITTNKGIFQTWQLSATNSHPTKLIDVNIYEAILESL QDLYPFAHGTLKIWDSHPLQDESSQLFLSSIYDSSCNETYYILSTIIFDSSSNSFTIFSTYRLNTFMESITDTKFKPKIF IPQMENANDTNEVTSILVMFPNAVVITQVNSKLDSSYSMRRKWEDIVSLRNDIDIIGSGYDSKSLYVLTKQMGVLQFFVK ENEETNSKPEVGFVKSHVDQAVYFSKINANPIDFNLPPEISLDQESIEHDLKLTSEEIFHSNGKYIPPMLNTLGQHLSVR KEFFQNFLTFVAKNFNYKISPELKLDLIEKFEILNCCIKFNSIIRQSDVLNDIWEKTLSNYNLTQNEHLTTKTVVINSPD VFPVIFKQFLNHVVFVLFPSQNQNFKLNVTNLINLCFYDGILEEGEKTIRYELLELDPMEVDTSKLPWFINFDYLNCINQ CFFDFTFACEEEGSLDSYKEGLLKIVKILYYQFNQFKIWINTQPVKSVNANDNFININNLYDDNHLDWNHVLCKVNLKEQ CIQIAEFYKDLSGLVQTLQTLDQNDSTTVSLYETFFNEFPKEFSFTLFEYLIKHKKLNDLIFRFPQQHDVLIQFFQESAP KYGHVAWIQQILDGSYADAMNTLKNITVDDSKKGESLSECELHLNVAKLSSLLVEKDNLDINTLRKIQYNLDTIDAEKNI SNKLKKGEVQICKRFKNGSIREVFNILVEELKSTTVVNLSDLVELYSMLDDEESLFIPLRLLSVDGNLLNFEVKKFLNAL VWRRIVLLNASNEGDKLLQHIVKRVFDEELPKNNDFPLPSVDLLCDKSLLTPEYISETYGRFPIDQNAIREEIYEEISQV ETLNSDNSLEIKLHSTIGSVAKEKNYTINYETNTVEY P36161 Dynein light chain 1, cytoplasmic Saccharomyces cerevisiae 0.01045698 6 LEVO MSDENKSTPIVKASDITDKLKEDILTISKDALDKYQLERDIAGTVKKQLDVKYGNTWHVIVGKNFGSYVTHEKGHFVYFY IGPLAFLVFKTA Q02647 subtomogramAveraging cell 7.5 Quantifoil R2/1 COPPER 200 GLOW DISCHARGE 60 0.039 ETHANE-PROPANE

A custom-built vitrification device (Max Planck Institute for Biochemistry, Munich).

W303 yeast cells were harvested during log-phase growth and diluted to an 0.8 x 107 cells/mL in YPD media. Five uL of this diluted sample was applied to glow-discharged 200-mesh, Quantafoil R2/1 grids (Electron Microscopy Sciences), excess media was manually blotted from the grid back side (opposite to the carbon substrate where the cells were deposited) and the grid was plunge frozen in a liquid ethane-propane mixture (50/50 volume, Airgas) then cryogenic, FIB milling was performed in an Aquilos DualBeam (Thermo Fisher Scientific)

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.5 2.5 6.0 6.0 42000.0 NITROGEN GIF Quantum LS 20

Tilt series collection: dose-symmetric & bi-directional

GATAN K2 SUMMIT (4k x 4k) COUNTING 3838 3708 2.0 4.5

Images were collected in movie-mode at ~8 frames per second

The tilt images were motion-corrected but not dose-weighted.

1 C8 FOURIER SPACE 37.0 FSC 0.143 CUT-OFF EMAN2 2.9 518 293 577 Manual boxing

The full nuclear pores were manually identified in the tomograms for the manual boxing.

NOT APPLICABLE emd_24258.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 2156.7998 2156.7998 2156.7998 90.0 90.0 90.0 X Y Z -3.9280643 4082.771200000000135 1772.169699999999921 428.825159999999983 6.7399993 6.7399993 6.7399993 1950.0 AUTHOR ::::EMDATABANK.org::::EMD-24258:::: full in situ NPC map recombined from 90 degree wedge focused alignment FLEXIBLE FIT

Manual docking and limited molecular dynamics flexible fitting

cross-correlation REAL emd_24258_msk_3.map emd_24258_msk_2.map emd_24258_msk_1.map emd_24258_additional_7.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 2156.7998 2156.7998 2156.7998 90.0 90.0 90.0 X Y Z -6273.809599999999591 3682.800299999999879 58.553035999999999 307.182500000000005 6.7399993 6.7399993 6.7399993 AUTHOR ::::EMDATABANK.org::::EMD-24258:::: difference map for pore membrane emd_24258_additional_6.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 2156.7998 2156.7998 2156.7998 90.0 90.0 90.0 X Y Z -0.47850436 8707.527000000000044 1.991591 79.547389999999993 6.7399993 6.7399993 6.7399993 AUTHOR ::::EMDATABANK.org::::EMD-24258:::: zoned 3D map of Pom152 ring emd_24258_additional_5.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 2156.7998 2156.7998 2156.7998 90.0 90.0 90.0 X Y Z -3.908072 3559.132799999999861 9.32654 136.54249999999999 6.7399993 6.7399993 6.7399993 AUTHOR ::::EMDATABANK.org::::EMD-24258:::: zoned 3D map of C-ring plus Nup82 complex with 3 Dyn 2 dimers emd_24258_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 2156.7998 2156.7998 2156.7998 90.0 90.0 90.0 X Y Z -4.742985 2641.803199999999833 3.6750057 76.03134 6.7399993 6.7399993 6.7399993 AUTHOR ::::EMDATABANK.org::::EMD-24258:::: zoned 3D map of the N-ring emd_24258_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 2156.7998 2156.7998 2156.7998 90.0 90.0 90.0 X Y Z -0.68325 4045.297999999999774 67.360564999999994 366.061919999999986 6.7399993 6.7399993 6.7399993 AUTHOR ::::EMDATABANK.org::::EMD-24258:::: full in situ NPC map recombined from 90 degree wedge focused alignment and masked to remove central channel density emd_24258_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 2156.7998 2156.7998 2156.7998 90.0 90.0 90.0 X Y Z -4.9488697 4043.010299999999916 18.261348999999999 204.721419999999995 6.7399993 6.7399993 6.7399993 AUTHOR ::::EMDATABANK.org::::EMD-24258:::: zoned 3D map of inner ring of spokes emd_24258_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 2156.7998 2156.7998 2156.7998 90.0 90.0 90.0 X Y Z -5.9862022 3518.740999999999985 1.3035755 47.098557 6.7399993 6.7399993 6.7399993 AUTHOR ::::EMDATABANK.org::::EMD-24258:::: zoned 3D map of Nsp1-FG-connections emd_24258_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 208 208 208 0 0 0 208 208 208 1438.112 1438.112 1438.112 90.0 90.0 90.0 X Y Z 0.0 4095.0 1896.820600000000013 131.53846999999999 6.9140005 6.9140005 6.9140005 AUTHOR ::::EMDATABANK.org::::EMD-24258:::: half map emd_24258_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 208 208 208 0 0 0 208 208 208 1438.112 1438.112 1438.112 90.0 90.0 90.0 X Y Z 0.0 4095.0 1894.372200000000021 131.117719999999991 6.9140005 6.9140005 6.9140005 AUTHOR ::::EMDATABANK.org::::EMD-24258:::: half map