2023-10-11 REL RCSB RCSB RCSB 2023-07-19 2023-10-11 2023-10-11 2023-10-11 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) NIH R01 GM45377 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) NIH P41 GM109824 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) NIH R01 GM112108 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) NIH GM117212 United States Double nuclear outer ring of Nup84-complexes from the yeast NPC Akey CW Echeverria I Ouch C Fernandez-Martinez J Rout MP nuclear pore complex, nucleocytoplasmic transport, nucleoporin, membrane protein, translocase, TRANSPORT PROTEIN Akey CW Echeverria I Ouch C Nudelman I Shi Y Wang J Chait BT Sali A Fernandez-Martinez J Rout MP Implications of a multiscale structure of the yeast nuclear pore complex. Mol.Cell US 83 3283 3302.e5 2023 37738963 doi:10.1016/j.molcel.2023.08.025 1097-2765 2168 MOCEFL EMD-41117 other EM volume
Pom34-Pom152 membrane attachment site yeast NPC
 EMD-41114 other EM volume
Full nuclear double outer ring of the yeast NPC
 EMD-41116 other EM volume
Lumenal ring of the isolated yeast NPC
 EMD-41119 other EM volume
Cytoplasmic outer ring of the yeast NPC
 EMD-41120 other EM volume
Central transporter/plug yeast NPC
 EMD-41121 other EM volume
Double outer ring connectors of yeast NPC
 EMD-41122 other EM volume
Connectors in cytoplasmic outer ring of yeast NPC
 EMD-41123 other EM volume
Composite multiscale structure of the yeast NPC
 EMD-41300 other EM volume
Inner spoke ring of the yeast NPC
 8tie FULLOVERLAP Nuclear Pore Complex Nuclear Pore Complex 0 1 2 3 4 5 6 7
Protein A tagged Mlp1 pullout of NPC
Saccharomyces cerevisiae MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 MLP1-PPX-ProteinA::HIS5 nucleus nuclear envelope double Nup84 Y-complex 1 1 2 3 4 5 6 7
Nup84 Y-complexes in nuclear double outer ring
Saccharomyces cerevisiae MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 MLP1-PPX-ProteinA::HIS5 nucleus nuclear envelope Nucleoporin NUP120 Saccharomyces cerevisiae MATa ade2-1 ura3-1 his3-11 0.120560328
long arm of Nup84 Y-complex
2 LEVO MACLSRIDANLLQYYEKPEPNNTVDLYVSNNSNNNGLKEGDKSISTPVPQPYGSEYSNCLLLSNSEYICYHFSSRSTLLT FYPLSDAYHGKTINIHLPNASMNQRYTLTIQEVEQQLLVNVILKDGSFLTLQLPLSFLFSSANTLNGEWFHLQNPYDFTV RVPHFLFYVSPQFSVVFLEDGGLLGLKKVDGVHYEPLLFNDNSYLKSLTRFFSRSSKSDYDSVISCKLFHERYLIVLTQN CHLKIWDLTSFTLIQDYDMVSQSDSDPSHFRKVEAVGEYLSLYNNTLVTLLPLENGLFQMGTLLVDSSGILTYTFQNNIP TNLSASAIWSIVDLVLTRPLELNVEASYLNLIVLWKSGTASKLQILNVNDESFKNYEWIESVNKSLVDLQSEHDLDIVTK TGDVERGFCNLKSRYGTQIFERAQQILSENKIIMAHNEDEEYLANLETILRDVKTAFNEASSITLYGDEIILVNCFQPYN HSLYKLNTTVENWFYNMHSETDGSELFKYLRTLNGFASTLSNDVLRSISKKFLDIITGELPDSMTTVEKFTDIFKNCLEN QFEITNLKILFDELNSFDIPVVLNDLINNQMKPGIFWKKDFISAIKFDGFTSIISLESLHQLLSIHYRITLQVLLTFVLF DLDTEIFGQHISTLLDLHYKQFLLLNLYRQDKCLLAEVLLKDSSEFSFGVKFFNYGQLIAYIDSLNSNVYNASITENSFF MTFFRSYIIENTSHKNIRFFLENVECPFYLRHNEVQEFMFAMTLFSCGNFDQSYEIFQLHDYPEAINDKLPTFLEDLKSE NYHGDSIWKDLLCTFTVPYRHSAFYYQLSLLFDRNNSQEFALKCISKSAEYSLKEIQIEELQDFKEKQHIHYLNLLIHFR MFEEVLDVLRLGHECLSDTVRTNFLQLLLQEDIYSRDFFSTLLRLCNAHSDNGELYLRTVDIKIVDSILSQNLRSGDWEC FKKLYCFRMLNKSERAAAEVLYQYILMQADLDVIRKRKCYLMVINVLSSFDSAYDQWILNGSKVVTLTDLRDELRGL P35729 Nucleoporin NUP85 Saccharomyces cerevisiae 0.084972438
short arm of Nup84 Y-complex
2 LEVO MTIDDSNRLLMDVDQFDFLDDGTAQLSNNKTDEEEQLYKRDPVSGAILVPMTVNDQPIEKNGDKMPLKFKLGPLSYQNMA FITAKDKYKLYPVRIPRLDTSKEFSAYVSGLFEIYRDLGDDRVFNVPTIGVVNSNFAKEHNATVNLAMEAILNELEVFIG RVKDQDGRVNRFYELEESLTVLNCLRTMYFILDGQDVEENRSEFIESLLNWINRSDGEPDEEYIEQVFSVKDSTAGKKVF ETQYFWKLLNQLVLRGLLSQAIGCIERSDLLPYLSDTCAVSFDAVSDSIELLKQYPKDSSSTFREWKNLVLKLSQAFGSS ATDISGELRDYIEDFLLVIGGNQRKILQYSRTWYESFCGFLLYYIPSLELSAEYLQMSLEANVVDITNDWEQPCVDIISG KIHSILPVMESLDSCTAAFTAMICEAKGLIENIFEGEKNSDDYSNEDNEMLEDLFSYRNGMASYMLNSFAFELCSLGDKE LWPVAIGLIALSATGTRSAKKMVIAELLPHYPFVTNDDIEWMLSICVEWRLPEIAKEIYTTLGNQMLSAHNIIESIANFS RAGKYELVKSYSWLLFEASCMEGQKLDDPVLNAIVSKNSPAEDDVIIPQDILDCVVTNSMRQTLAPYAVLSQFYELRDRE DWGQALRLLLLLIEFPYLPKHYLVLLVAKFLYPIFLLDDKKLMDEDSVATVIEVIETKWDDADEKSSNLYETIIEADKSL PSSMATLLKNLRKKLNFKLCQAFM P46673 NUP145 isoform 1 Saccharomyces cerevisiae 0.145810578
stem junction of Nup84 Y-complex
2 LEVO MFNKSVNSGFTFGNQNTSTPTSTPAQPSSSLQFPQKSTGLFGNVNVNANTSTPSPSGGLFNANSNANSISQQPANNSLFG NKPAQPSGGLFGATNNTTSKSAGSLFGNNNATANSTGSTGLFSGSNNIASSTQNGGLFGNSNNNNITSTTQNGGLFGKPT TTPAGAGGLFGNSSSTNSTTGLFGSNNTQSSTGIFGQKPGASTTGGLFGNNGASFPRSGETTGTMSTNPYGINISNVPMA VADMPRSITSSLSDVNGKSDAEPKPIENRRTYSFSSSVSGNAPLPLASQSSLVSRLSTRLKATQKSTSPNEIFSPSYSKP WLNGAGSAPLVDDFFSSKMTSLAPNENSIFPQNGFNFLSSQRADLTELRKLKIDSNRSAAKKLKLLSGTPAITKKHMQDE QDSSENEPIANADSVTNIDRKENRDNNLDNTYLNGKEQSNNLNKQDGENTLQHEKSSSFGYWCSPSPEQLERLSLKQLAA VSNFVIGRRGYGCITFQHDVDLTAFTKSFREELFGKIVIFRSSKTVEVYPDEATKPMIGHGLNVPAIITLENVYPVDKKT KKPMKDTTKFAEFQVFDRKLRSMREMNYISYNPFGGTWTFKVNHFSIWGLVNEEDAEIDEDDLSKQEDGGEQPLRKVRTL AQSKPSDKEVILKTDGTFGTLSGKDDSIVEEKAYEPDLSDADFEGIEASPKLDVSKDWVEQLILAGSSLRSVFATSKEFD GPCQNEIDLLFSECNDEIDNAKLIMKERRFTASYTFAKFSTGSMLLTKDIVGKSGVSIKRLPTELQRKFLFDDVYLDKEI EKVTIEARKSNPYPQISESSLLFKDALDYMEKTSSDYNLWKLSSILFDPVSYPYKTDNDQVKMALLKKERHCRLTSWIVS QIGPEIEEKIRNSSNEIEQIFLYLLLNDVVRASKLAIESKNGHLSVLISYLGSNDPRIRDLAELQLQKWSTGGCSIDKNI SKIYKLLSGSPFEGLFSLKELESEFSWLCLLNLTLCYGQIDEYSLESLVQSHLDKFSLPYDDPIGVIFQLYAANENTEKL YKEVRQRTNALDVQFCWYLIQTLRFNGTRVFSKETSDEATFAFAAQLEFAQLHGHSLFVSCFLNDDKAAEDTIKRLVMRE ITLLRASTNDHILNRLKIPSQLIFNAQALKDRYEGNYLSEVQNLLLGSSYDLAEMAIVTSLGPRLLLSNNPVQNNELKTL REILNEFPDSERDKWSVSINVFEVYLKLVLDNVETQETIDSLISGMKIFYDQYKHCREVAACCNVMSQEIVSKILEKNNP SIGDSKAKLLELPLGQPEKAYLRGEFAQDLMKCTYKI A0A8H4C085 Protein transport protein SEC13 Saccharomyces cerevisiae 0.03308296499999999
cofactor of Nup145C on stem of Nup84 Y-complex
2 LEVO MVVIANAHNELIHDAVLDYYGKRLATCSSDKTIKIFEVEGETHKLIDTLTGHEGPVWRVDWAHPKFGTILASCSYDGKVL IWKEENGRWSQIAVHAVHSASVNSVQWAPHEYGPLLLVASSDGKVSVVEFKENGTTSPIIIDAHAIGVNSASWAPATIEE DGEHNGTKESRKFVTGGADNLVKIWKYNSDAQTYVLESTLEGHSDWVRDVAWSPTVLLRSYLASVSQDRTCIIWTQDNEQ GPWKKTLLKEEKFPDVLWRASWSLSGNVLALSGGDNKVTLWKENLEGKWEPAGEVHQ Q04491 Nucleoporin Seh1 Saccharomyces cerevisiae 0.034652078
cofactor Nup85
2 LEVO MQPFDSGHDDLVHDVVYDFYGRHVATCSSDQHIKVFKLDKDTSNWELSDSWRAHDSSIVAIDWASPEYGRIIASASYDKT VKLWEEDPDQEECSGRRWNKLCTLNDSKGSLYSVKFAPAHLGLKLACLGNDGILRLYDALEPSDLRSWTLTSEMKVLSIP PANHLQSDFCLSWCPSRFSPEKLAVSALEQAIIYQRGKDGKLHVAAKLPGHKSLIRSISWAPSIGRWYQLIATGCKDGRI RIFKITEKNLQVELLSEHDDHNGEVWSVSWNLTGTILSSAGDDGKVRLWKATYSNEFKCMSVITAQQ Nucleoporin NUP84 Saccharomyces cerevisiae 0.08371886699999999
tail of Nup84 Y-complex
2 LEVO MELSPTYQTERFTKFSDTLKEFKIEQNNEQNPIDPFNIIREFRSAAGQLALDLANSGDESNVISSKDWELEARFWHLVEL LLVFRNADLDLDEMELHPYNSRGLFEKKLMQDNKQLYQIWIVMVWLKENTYVMERPKNVPTSKWLNSITSGGLKSCDLDF PLRENTNVLDVKDKEEDHIFFKYIYELILAGAIDEALEEAKLSDNISICMILCGIQEYLNPVIDTQIANEFNTQQGIKKH SLWRRTVYSLSQQAGLDPYERAIYSYLSGAIPNQEVLQYSDWESDLHIHLNQILQTEIENYLLENNQVGTDELILPLPSH ALTVQEVLNRVASRHPSESEHPIRVLMASVILDSLPSVIHSSVEMLLDVVKGTEASNDIIDKPYLLRIVTHLAICLDIIN PGSVEEVDKSKLITTYISLLKLQGLYENIPIYATFLNESDCLEACSFILSSLEDPQVRKKQIETINFLRLPASNILRRTT QRVFDETEQEYSPSNEISISFDVNNIDMHLIYGVEWLIEGKLYVDAVHSIIALSRRFLLNGRVKALEQFMERNNIGEICK NYELEKIADNISKDENEDQFLEEITQYEHLIKGIREYEEWQKSVSLLSSESNIPTLIEKLQGFSKDTFELIKTFLVDLTS SNFADSADYEILYEIRALYTPFLLMELHKKLVEAAKLLKIPKFISEALAFTSLVANENDKIYLLFQSSGKLKEYLDLVAR TATLSN P52891 NUP133 isoform 1 Saccharomyces cerevisiae 0.133452672
tail Nup84 Y-complex
2 LEVO MSEKKVHLRLRKELSVPIAVVENESLAQLSYEEESQASLMDISMEQQQLRLHSHFDNSKVFTENNRYIVKTLQTDYSSGF SNDDELNGYIDMQIGYGLVNDHKKVYIWNIHSTQKDTPYITVPFRSDDNDEIAVAPRCILTFPATMDESPLALNPNDQDE TGGLIIIKGSKAIYYEDINSINNLNFKLSEKFSHELELPINSSGGEKCDLMLNCEPAGIVLSTNMGRIFFITIRNSMGKP QLKLGKLLNKPFKLGIWSKIFNTNSSVVSLRNGPILGKGTRLVYITTNKGIFQTWQLSATNSHPTKLIDVNIYEAILESL QDLYPFAHGTLKIWDSHPLQDESSQLFLSSIYDSSCNETYYILSTIIFDSSSNSFTIFSTYRLNTFMESITDTKFKPKIF IPQMENANDTNEVTSILVMFPNAVVITQVNSKLDSSYSMRRKWEDIVSLRNDIDIIGSGYDSKSLYVLTKQMGVLQFFVK ENEETNSKPEVGFVKSHVDQAVYFSKINANPIDFNLPPEISLDQESIEHDLKLTSEEIFHSNGKYIPPMLNTLGQHLSVR KEFFQNFLTFVAKNFNYKISPELKLDLIEKFEILNCCIKFNSIIRQSDVLNDIWEKTLSNYNLTQNEHLTTKTVVINSPD VFPVIFKQFLNHVVFVLFPSQNQNFKLNVTNLINLCFYDGILEEGEKTIRYELLELDPMEVDTSKLPWFINFDYLNCINQ CFFDFTFACEEEGSLDSYKEGLLKIVKILYYQFNQFKIWINTQPVKSVNANDNFININNLYDDNHLDWNHVLCKVNLKEQ CIQIAEFYKDLSGLVQTLQTLDQNDSTTVSLYETFFNEFPKEFSFTLFEYLIKHKKLNDLIFRFPQQHDVLIQFFQESAP KYGHVAWIQQILDGSYADAMNTLKNITVDDSKKGESLSECELHLNVAKLSSLLVEKDNLDINTLRKIQYNLDTIDAEKNI SNKLKKGEVQICKRFKNGSIREVFNILVEELKSTTVVNLSDLVELYSMLDDEESLFIPLRLLSVDGNLLNFEVKKFLNAL VWRRIVLLNASNEGDKLLQHIVKRVFDEELPKNNDFPLPSVDLLCDKSLLTPEYISETYGRFPIDQNAIREEIYEEISQV ETLNSDNSLEIKLHSTIGSVAKEKNYTINYETNTVEY A0A6V8RYD2 singleParticle particle 0.1 7.5
20mM HEPES,50mM Potassium acetate,20mM NaCl,2mM MgCl2,1mM DTT
 ETHANE 100 283 FEI VITROBOT MARK III
One step affinity purified
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 1.5 3.5 37651.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20
Preliminary grid screening done manually with individual images of low magnification montages of candidate meshes.
GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 3838 3710 2-40 1 4015 40.0
3218 images retained after triage
 1 26049
C8 symmetrized NPC map segmented in CHIMERA with Segger to provide initial 3D map of the double outer ring, which was low pass filtered for the first reference.
 C1 FOURIER SPACE 8.1 FSC 0.143 CUT-OFF cryoSPARC 3.3.2 non-uniform refinement
multibody in RELION followed by refinements in cryosparc
29655 MAXIMUM LIKELIHOOD RELION 3.0.7
C8 symmetry used followed by Multibody processing focused on a double Y-complex protomer
 MAXIMUM LIKELIHOOD cryoSPARC 3.3.2 non-uniform refinement
C1 symmetry used to refine to refine double Y-complex protomer
 RELION 3.0.7 emd_41285.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 -1.568928 6.037515 0.0061389585 0.083342575 2.66 2.66 2.66 0.4 AUTHOR full c8 ring of double Y-complexes from multibody volume Other experimental model
none
 FLEXIBLE FIT
Molecular dynamics flexible fitting after docking Alphafold2 CSMs for Nups into the 3D map of double Y complex ring with Chimera
cross correlation REAL emd_41285_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 1197.0 1197.0 1197.0 90.0 90.0 90.0 X Y Z -2.255711 5.323481 0.0011224765 0.038237084 3.99 3.99 3.99 AUTHOR multibody half map emd_41285_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 -1.2730007 5.318064 0.0007284323 0.028673196 2.66 2.66 2.66 AUTHOR recombined 2 Y-complex protomer, bfactor -600 and local resolution box 120 emd_41285_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 1197.0 1197.0 1197.0 90.0 90.0 90.0 X Y Z -2.5475426 5.709287 0.0011149389 0.038127962 3.99 3.99 3.99 AUTHOR multibody half map emd_41285_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 1197.0 1197.0 1197.0 90.0 90.0 90.0 X Y Z -5.349573 9.119949999999999 0.0011522865 0.048214015 3.99 3.99 3.99 AUTHOR post processed multibody volume emd_41285_half_map_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 -2.091934 7.3077774 0.008770848 0.102643564 2.66 2.66 2.66 AUTHOR half map of c8 ring emd_41285_half_map_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 -1.7260857 7.252015 0.008843003 0.10285281 2.66 2.66 2.66 AUTHOR half map of c8 ring