2025-11-12 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update DATA_COLLECTION chem_comp_atom chem_comp_bond STRUCTURE_SUMMARY audit_author em_admin pdbx_entry_details _audit_author.name _em_admin.last_update _pdbx_entry_details.has_protein_modification RCSB RCSB 2021-06-13 2022-01-26 2022-01-26 2025-11-12 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01 GM45377 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01 GM112108 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) P41 GM109824 United States Double nuclear outer ring from the isolated yeast NPC Akey CW Rout MP nuclear pore complex, outer ring, Nup84 complex, 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-24232 other EM volume
inner ring of spokes
 EMD-24225 other EM volume
low resolution NPC maps
 EMD-24224 other EM volume
combined yeast NPC maps
 EMD-24258 other EM volume
in situ yeast NPC maps
 7n84 FULLOVERLAP EMDB EMD-24231 associated EM volume
Double nuclear outer ring from the isolated yeast NPC
 EMDB EMD-24232 other EM volume
inner ring of spokes
 EMDB EMD-24225 other EM volume
low resolution NPC maps
 EMDB EMD-24224 other EM volume
combined yeast NPC maps
 EMDB EMD-24258 other EM volume
in situ yeast NPC maps
 PDB 7N85 unspecified
spoke model
 PDB 7N9F unspecified
in situ C8 protomer model
 yeast double outer ring yeast double outer ring 0 1 2 3 4 5 6 7 8 9
Novel outer ring C8 protomer with two copies of Nup84 complex, one copy of Nup188 and an unknown basket anchor model
Saccharomyces cerevisiae nuclear envelope 10.4 Nucleoporin NUP188 Saccharomyces cerevisiae 0.18875328099999997 1 LEVO MATPSFGNSSPQLTFTHVANFMNDAAADVSAVDAKQLAQIRQFLKANKTNLIESLNTIRQNVTSSGDHNKLRSTIANLLQ INVDNDPFFAQSEDLSHAVEFFMSERSSRLHIVYSLLVNPDIDLETYSFIDNDRFNVVGKLISIISSVIQNYDIITASSL AHDYNNDQDMFTIVSLVQLKKFSDLKFILQILQILNLMILNTKVPVDIVNQWFLQYQNQFVEFCRNINSTDKSIDTSSLQ LYKFQNFQDLSYLSETLISRISSLFTITTILILGLNTSIAQFDIQSPLYMDTETFDTVNSALENDVATNIVNEDPIFHPM IHYSWSFILYYRRALQSSESFDDSDITKFALFAESHDVLQKLNTLSEILSFDPVYTTVITVFLEFSLNFIPITASTSRVF AKIISKAPEQFIENFLTNDTFEKKLSIIKAKLPLLNESLIPLINLALIDTEFANFELKDICSFAVTKSSLNDLDYDLIAD TITNSSSSSDIIVPDLIELKSDLLVAPPLENENSNCLLSIPKSTKGKILTIKQQQQQQQQQNGQQPPTTSNLIIFLYKFN GWSLVGRILQNLLHSYMEKGTQLDDLQHELMISIIKLVTNVVDPKTSIEKSSEILSYLSNSLDTSASTINGASIIQVIFE IFEISLQRKDYTSIVQCCEFMTMLTPNYLHLVSSYLNKSDLLDKYGKTGLSNMILGSVELSTGDYTFTIQLLKLTKVFIR ESLSLKNIHISKRSKIDIINKLILHAIHIFESYYNWKYNNFLQKFEIAFHLTLIFYDVLHDVFTINPHQKDQLIISSSAN KLLQLFLTPMDSIDLAPNTLTNILISPLNTTTKILGDKILGNLYSKVMNNSFKLCTLLIAIRGSNRDLKPSNLEKLLFIN SSKLVDVYTLPSYVHFKVQIIELLSYLVEAPWNDDYPFLLSFLGEAKSMAFLKEVLSDLSSPVQDWNLLRSLYIFFTTLL ESKQDGLSILFLTGQFASNKKINDESSIDKKSSILTVLQKNSLLLDSTPEEVSCKLLETITYVLNTWTNSKIFIKDPKFV NSLLAKLKDSKKLFQKKENLTRDETVSLIKKYKLISRIVEIFALCIYNSTDSNSEILNFLNQEDLFELVHHFFQIDGFNK TFHDELNLKFKEKWPSLELQSFQKIPLSRINENENFGYDIPLLDIVLKADRSWNEPSKSQTNFKEEITDASLNLQYVNYE ISTAKAWGALITTFVKRSTVPLNDGFVDLVEHFLKLNIDFGSDKQMFTQIYLERIELSFYILYSFKLSGKLLKEEKIIEL MNKIFTIFKSGEIDFIKNIGKSLKNNFYRPLLRSVLVLLELVSSGDRFIELISDQLLEFFELVFSKGVYLILSEILCQIN KCSTRGLSTDHTTQIVNLEDNTQDLLLLLSLFKKITNVNPSKNFNVILASSLNEVGTLKVILNLYSSAHLIRINDEPILG QITLTFISELCSIEPIAAKLINSGLYSVLLESPLSVAIQQGDIKPEFSPRLHNIWSNGLLSIVLLLLSQFGIKVLPETCL FVSYFGKQIKSTIYNWGDNKLAVSSSLIKETNQLVLLQKMLNLLNYQELFIQPKNSDDQQEAVELVIGLDSEHDKKRLSA ALSKFLTHPKYLNSRIIPTTLEEQQQLEDESSRLEFVKGISRDIKALQDSLFKDV P52593 unknown Saccharomyces cerevisiae 0.005379622999999999 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)(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 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 singleParticle particle 0.3 7.5 20.0 HEPES 50.0 potassium acetate 20.0 NaCl sodium chloride 2.0 magnesium chloride 1.0 DTT 0.1 DeoxyBigChaps Quantifoil R2/2 COPPER 400 CARBON CONTINUOUS 5.0 GLOW DISCHARGE AIR ETHANE 100 283 FEI VITROBOT MARK III
double outer ring imaged from isolated yeast NPC
 FEI TITAN KRIOS OTHER BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 1.5 3.8000000000000003 50000.0 37651.0 NITROGEN GIF Bioquantum 20 GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 3838 3710 2-40 1 4015 40.0 1 Gctf 1.18 PHASE FLIPPING ONLY EMD-7321 C1 FOURIER SPACE 11.6 FSC 0.143 CUT-OFF RELION 3.0
gold standard in RELION
45000 MAXIMUM LIKELIHOOD RELION 2.0 MAXIMUM LIKELIHOOD RELION 3.0 RELION 3.0 emd_24231.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 1276.8 1276.8 1276.8 90.0 90.0 90.0 X Y Z -0.01903938 0.1297321 0.0007293956 0.0062733702 2.66 2.66 2.66 0.01 AUTHOR recombined double nuclear outer ring FLEXIBLE FIT
molecular dynamics flexible fitting
REAL emd_24231_msk_1.map emd_24231_additional_5.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 1276.8 1276.8 1276.8 90.0 90.0 90.0 X Y Z -0.000000006781684 0.063414276 0.0000044344456 0.00034030346 2.66 2.66 2.66 AUTHOR zoned putative basket density ring emd_24231_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 1276.8 1276.8 1276.8 90.0 90.0 90.0 X Y Z -0.000125504 0.0771211 0.00003597426 0.001071839 2.66 2.66 2.66 AUTHOR zoned Nup188-192 density ring emd_24231_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 1194.0 1194.0 1194.0 90.0 90.0 90.0 X Y Z -0.8288432 2.6111808 0.0017767595 0.044350643 3.98 3.98 3.98 AUTHOR post processed multibody for double nuclear outer ring emd_24231_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 1276.8 1276.8 1276.8 90.0 90.0 90.0 X Y Z -0.010073939 0.11301593 0.00029994998 0.0040743146 2.66 2.66 2.66 AUTHOR zoned proximal outer nuclear ring emd_24231_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 1276.8 1276.8 1276.8 90.0 90.0 90.0 X Y Z -0.009485853 0.118635334 0.00031139597 0.004193791 2.66 2.66 2.66 AUTHOR zoned proximal outer nuclear ring emd_24231_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 1194.0 1194.0 1194.0 90.0 90.0 90.0 X Y Z -0.0477403 0.13114004 0.00008608478 0.0040295366 3.98 3.98 3.98 AUTHOR half map for double Y multibody emd_24231_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 1194.0 1194.0 1194.0 90.0 90.0 90.0 X Y Z -0.052033067 0.12474003 0.000092627626 0.0040504155 3.98 3.98 3.98 AUTHOR half map for double Y multibody