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- EMDB-41285: Double nuclear outer ring of Nup84-complexes from the yeast NPC -

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Basic information

Entry
Database: EMDB / ID: EMD-41285
TitleDouble nuclear outer ring of Nup84-complexes from the yeast NPC
Map datafull c8 ring of double Y-complexes from multibody volume
Sample
  • Complex: Nuclear Pore ComplexNuclear pore
    • Complex: double Nup84 Y-complex
      • Protein or peptide: Nucleoporin NUP120
      • Protein or peptide: Nucleoporin NUP85
      • Protein or peptide: NUP145 isoform 1
      • Protein or peptide: Protein transport protein SEC13Protein targeting
      • Protein or peptide: Nucleoporin Seh1
      • Protein or peptide: Nucleoporin NUP84
      • Protein or peptide: NUP133 isoform 1
Keywordsnuclear pore complex / nucleocytoplasmic transport / nucleoporin / membrane protein / translocase / TRANSPORT PROTEIN
Function / homology
Function and homology information


mRNA export from nucleus in response to heat stress / Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / COPII-mediated vesicle transport / nuclear pore localization / nuclear pore central transport channel / telomere tethering at nuclear periphery / regulation of TORC1 signaling ...mRNA export from nucleus in response to heat stress / Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / COPII-mediated vesicle transport / nuclear pore localization / nuclear pore central transport channel / telomere tethering at nuclear periphery / regulation of TORC1 signaling / nuclear pore outer ring / COPII vesicle coat / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / positive regulation of protein exit from endoplasmic reticulum / structural constituent of nuclear pore / vacuolar membrane / silent mating-type cassette heterochromatin formation / nucleocytoplasmic transport / subtelomeric heterochromatin formation / ribosomal large subunit export from nucleus / positive regulation of TOR signaling / mRNA transport / mRNA export from nucleus / nuclear pore / : / positive regulation of TORC1 signaling / protein export from nucleus / cell periphery / protein import into nucleus / double-strand break repair / nuclear envelope / nuclear membrane / chromosome, telomeric region / endoplasmic reticulum membrane / structural molecule activity / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / identical protein binding
Similarity search - Function
Nucleoporin Nup85-like / Nucleoporin Nup120/160 / Nup85 Nucleoporin / Nuclear pore protein 84/107 / Nuclear pore protein 84 / 107 / Nuclear pore complex protein Nup133-like / Nucleoporin FG repeat / Nucleoporin FG repeat region / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like ...Nucleoporin Nup85-like / Nucleoporin Nup120/160 / Nup85 Nucleoporin / Nuclear pore protein 84/107 / Nuclear pore protein 84 / 107 / Nuclear pore complex protein Nup133-like / Nucleoporin FG repeat / Nucleoporin FG repeat region / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like / Sec13/Seh1 family / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin autopeptidase / NUP C-terminal domain profile. / Nucleoporin peptidase S59-like / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
NUP133 isoform 1 / NUP145 isoform 1 / Nucleoporin NUP120 / Nucleoporin NUP85 / Nucleoporin NUP84 / Protein transport protein SEC13
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.1 Å
AuthorsAkey CW / Echeverria I / Ouch C / Fernandez-Martinez J / Rout MP
Funding support United States, 4 items
OrganizationGrant numberCountry
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
CitationJournal: Mol Cell / Year: 2023
Title: Implications of a multiscale structure of the yeast nuclear pore complex.
Authors: Christopher W Akey / Ignacia Echeverria / Christna Ouch / Ilona Nudelman / Yi Shi / Junjie Wang / Brian T Chait / Andrej Sali / Javier Fernandez-Martinez / Michael P Rout /
Abstract: Nuclear pore complexes (NPCs) direct the nucleocytoplasmic transport of macromolecules. Here, we provide a composite multiscale structure of the yeast NPC, based on improved 3D density maps from ...Nuclear pore complexes (NPCs) direct the nucleocytoplasmic transport of macromolecules. Here, we provide a composite multiscale structure of the yeast NPC, based on improved 3D density maps from cryogenic electron microscopy and AlphaFold2 models. Key features of the inner and outer rings were integrated into a comprehensive model. We resolved flexible connectors that tie together the core scaffold, along with equatorial transmembrane complexes and a lumenal ring that anchor this channel within the pore membrane. The organization of the nuclear double outer ring reveals an architecture that may be shared with ancestral NPCs. Additional connections between the core scaffold and the central transporter suggest that under certain conditions, a degree of local organization is present at the periphery of the transport machinery. These connectors may couple conformational changes in the scaffold to the central transporter to modulate transport. Collectively, this analysis provides insights into assembly, transport, and NPC evolution.
History
DepositionJul 19, 2023-
Header (metadata) releaseOct 11, 2023-
Map releaseOct 11, 2023-
UpdateOct 11, 2023-
Current statusOct 11, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41285.png

Downloads & links

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Map

FileDownload / File: emd_41285.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull c8 ring of double Y-complexes from multibody volume
Voxel sizeX=Y=Z: 2.66 Å
Density
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.568928 - 6.037515
Average (Standard dev.)0.0061389585 (±0.083342575)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 1276.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: multibody half map

Fileemd_41285_additional_1.map
Annotationmultibody half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: recombined 2 Y-complex protomer, bfactor -600 and local...

Fileemd_41285_additional_2.map
Annotationrecombined 2 Y-complex protomer, bfactor -600 and local resolution box 120
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: multibody half map

Fileemd_41285_additional_3.map
Annotationmultibody half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: post processed multibody volume

Fileemd_41285_additional_4.map
Annotationpost processed multibody volume
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map of c8 ring

Fileemd_41285_half_map_1.map
Annotationhalf map of c8 ring
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map of c8 ring

Fileemd_41285_half_map_2.map
Annotationhalf map of c8 ring
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Nuclear Pore Complex

EntireName: Nuclear Pore ComplexNuclear pore
Components
  • Complex: Nuclear Pore ComplexNuclear pore
    • Complex: double Nup84 Y-complex
      • Protein or peptide: Nucleoporin NUP120
      • Protein or peptide: Nucleoporin NUP85
      • Protein or peptide: NUP145 isoform 1
      • Protein or peptide: Protein transport protein SEC13Protein targeting
      • Protein or peptide: Nucleoporin Seh1
      • Protein or peptide: Nucleoporin NUP84
      • Protein or peptide: NUP133 isoform 1

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Supramolecule #1: Nuclear Pore Complex

SupramoleculeName: Nuclear Pore Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Protein A tagged Mlp1 pullout of NPC
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Strain: MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 MLP1-PPX-ProteinA::HIS5
Organelle: nucleus / Location in cell: nuclear envelope

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Supramolecule #2: double Nup84 Y-complex

SupramoleculeName: double Nup84 Y-complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all / Details: Nup84 Y-complexes in nuclear double outer ring
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Strain: MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 MLP1-PPX-ProteinA::HIS5
Organelle: nucleus / Location in cell: nuclear envelope

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Macromolecule #1: Nucleoporin NUP120

MacromoleculeName: Nucleoporin NUP120 / type: protein_or_peptide / ID: 1 / Details: long arm of Nup84 Y-complex / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: MATa ade2-1 ura3-1 his3-11
Molecular weightTheoretical: 120.560328 KDa
SequenceString: MACLSRIDAN LLQYYEKPEP NNTVDLYVSN NSNNNGLKEG DKSISTPVPQ PYGSEYSNCL LLSNSEYICY HFSSRSTLLT FYPLSDAYH GKTINIHLPN ASMNQRYTLT IQEVEQQLLV NVILKDGSFL TLQLPLSFLF SSANTLNGEW FHLQNPYDFT V RVPHFLFY ...String:
MACLSRIDAN LLQYYEKPEP NNTVDLYVSN NSNNNGLKEG DKSISTPVPQ PYGSEYSNCL LLSNSEYICY HFSSRSTLLT FYPLSDAYH GKTINIHLPN ASMNQRYTLT IQEVEQQLLV NVILKDGSFL TLQLPLSFLF SSANTLNGEW FHLQNPYDFT V RVPHFLFY VSPQFSVVFL EDGGLLGLKK VDGVHYEPLL FNDNSYLKSL TRFFSRSSKS DYDSVISCKL FHERYLIVLT QN CHLKIWD LTSFTLIQDY DMVSQSDSDP SHFRKVEAVG EYLSLYNNTL VTLLPLENGL FQMGTLLVDS SGILTYTFQN NIP TNLSAS AIWSIVDLVL TRPLELNVEA SYLNLIVLWK SGTASKLQIL NVNDESFKNY EWIESVNKSL VDLQSEHDLD IVTK TGDVE RGFCNLKSRY GTQIFERAQQ ILSENKIIMA HNEDEEYLAN LETILRDVKT AFNEASSITL YGDEIILVNC FQPYN HSLY KLNTTVENWF YNMHSETDGS ELFKYLRTLN GFASTLSNDV LRSISKKFLD IITGELPDSM TTVEKFTDIF KNCLEN QFE ITNLKILFDE LNSFDIPVVL NDLINNQMKP GIFWKKDFIS AIKFDGFTSI ISLESLHQLL SIHYRITLQV LLTFVLF DL DTEIFGQHIS TLLDLHYKQF LLLNLYRQDK CLLAEVLLKD SSEFSFGVKF FNYGQLIAYI DSLNSNVYNA SITENSFF M TFFRSYIIEN TSHKNIRFFL ENVECPFYLR HNEVQEFMFA MTLFSCGNFD QSYEIFQLHD YPEAINDKLP TFLEDLKSE NYHGDSIWKD LLCTFTVPYR HSAFYYQLSL LFDRNNSQEF ALKCISKSAE YSLKEIQIEE LQDFKEKQHI HYLNLLIHFR MFEEVLDVL RLGHECLSDT VRTNFLQLLL QEDIYSRDFF STLLRLCNAH SDNGELYLRT VDIKIVDSIL SQNLRSGDWE C FKKLYCFR MLNKSERAAA EVLYQYILMQ ADLDVIRKRK CYLMVINVLS SFDSAYDQWI LNGSKVVTLT DLRDELRGL

UniProtKB: Nucleoporin NUP120

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Macromolecule #2: Nucleoporin NUP85

MacromoleculeName: Nucleoporin NUP85 / type: protein_or_peptide / ID: 2 / Details: short arm of Nup84 Y-complex / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 84.972438 KDa
SequenceString: MTIDDSNRLL MDVDQFDFLD DGTAQLSNNK TDEEEQLYKR DPVSGAILVP MTVNDQPIEK NGDKMPLKFK LGPLSYQNMA FITAKDKYK LYPVRIPRLD TSKEFSAYVS GLFEIYRDLG DDRVFNVPTI GVVNSNFAKE HNATVNLAME AILNELEVFI G RVKDQDGR ...String:
MTIDDSNRLL MDVDQFDFLD DGTAQLSNNK TDEEEQLYKR DPVSGAILVP MTVNDQPIEK NGDKMPLKFK LGPLSYQNMA FITAKDKYK LYPVRIPRLD TSKEFSAYVS GLFEIYRDLG DDRVFNVPTI GVVNSNFAKE HNATVNLAME AILNELEVFI G RVKDQDGR VNRFYELEES LTVLNCLRTM YFILDGQDVE ENRSEFIESL LNWINRSDGE PDEEYIEQVF SVKDSTAGKK VF ETQYFWK LLNQLVLRGL LSQAIGCIER SDLLPYLSDT CAVSFDAVSD SIELLKQYPK DSSSTFREWK NLVLKLSQAF GSS ATDISG ELRDYIEDFL LVIGGNQRKI LQYSRTWYES FCGFLLYYIP SLELSAEYLQ MSLEANVVDI TNDWEQPCVD IISG KIHSI LPVMESLDSC TAAFTAMICE AKGLIENIFE GEKNSDDYSN EDNEMLEDLF SYRNGMASYM LNSFAFELCS LGDKE LWPV AIGLIALSAT GTRSAKKMVI AELLPHYPFV TNDDIEWMLS ICVEWRLPEI AKEIYTTLGN QMLSAHNIIE SIANFS RAG KYELVKSYSW LLFEASCMEG QKLDDPVLNA IVSKNSPAED DVIIPQDILD CVVTNSMRQT LAPYAVLSQF YELRDRE DW GQALRLLLLL IEFPYLPKHY LVLLVAKFLY PIFLLDDKKL MDEDSVATVI EVIETKWDDA DEKSSNLYET IIEADKSL P SSMATLLKNL RKKLNFKLCQ AFM

UniProtKB: Nucleoporin NUP85

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Macromolecule #3: NUP145 isoform 1

MacromoleculeName: NUP145 isoform 1 / type: protein_or_peptide / ID: 3 / Details: stem junction of Nup84 Y-complex / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 145.810578 KDa
SequenceString: MFNKSVNSGF TFGNQNTSTP TSTPAQPSSS LQFPQKSTGL FGNVNVNANT STPSPSGGLF NANSNANSIS QQPANNSLFG NKPAQPSGG LFGATNNTTS KSAGSLFGNN NATANSTGST GLFSGSNNIA SSTQNGGLFG NSNNNNITST TQNGGLFGKP T TTPAGAGG ...String:
MFNKSVNSGF TFGNQNTSTP TSTPAQPSSS LQFPQKSTGL FGNVNVNANT STPSPSGGLF NANSNANSIS QQPANNSLFG NKPAQPSGG LFGATNNTTS KSAGSLFGNN NATANSTGST GLFSGSNNIA SSTQNGGLFG NSNNNNITST TQNGGLFGKP T TTPAGAGG LFGNSSSTNS TTGLFGSNNT QSSTGIFGQK PGASTTGGLF GNNGASFPRS GETTGTMSTN PYGINISNVP MA VADMPRS ITSSLSDVNG KSDAEPKPIE NRRTYSFSSS VSGNAPLPLA SQSSLVSRLS TRLKATQKST SPNEIFSPSY SKP WLNGAG SAPLVDDFFS SKMTSLAPNE NSIFPQNGFN FLSSQRADLT ELRKLKIDSN RSAAKKLKLL SGTPAITKKH MQDE QDSSE NEPIANADSV TNIDRKENRD NNLDNTYLNG KEQSNNLNKQ DGENTLQHEK SSSFGYWCSP SPEQLERLSL KQLAA VSNF VIGRRGYGCI TFQHDVDLTA FTKSFREELF GKIVIFRSSK TVEVYPDEAT KPMIGHGLNV PAIITLENVY PVDKKT KKP MKDTTKFAEF QVFDRKLRSM REMNYISYNP FGGTWTFKVN HFSIWGLVNE EDAEIDEDDL SKQEDGGEQP LRKVRTL AQ SKPSDKEVIL KTDGTFGTLS GKDDSIVEEK AYEPDLSDAD FEGIEASPKL DVSKDWVEQL ILAGSSLRSV FATSKEFD G PCQNEIDLLF SECNDEIDNA KLIMKERRFT ASYTFAKFST GSMLLTKDIV GKSGVSIKRL PTELQRKFLF DDVYLDKEI EKVTIEARKS NPYPQISESS LLFKDALDYM EKTSSDYNLW KLSSILFDPV SYPYKTDNDQ VKMALLKKER HCRLTSWIVS QIGPEIEEK IRNSSNEIEQ IFLYLLLNDV VRASKLAIES KNGHLSVLIS YLGSNDPRIR DLAELQLQKW STGGCSIDKN I SKIYKLLS GSPFEGLFSL KELESEFSWL CLLNLTLCYG QIDEYSLESL VQSHLDKFSL PYDDPIGVIF QLYAANENTE KL YKEVRQR TNALDVQFCW YLIQTLRFNG TRVFSKETSD EATFAFAAQL EFAQLHGHSL FVSCFLNDDK AAEDTIKRLV MRE ITLLRA STNDHILNRL KIPSQLIFNA QALKDRYEGN YLSEVQNLLL GSSYDLAEMA IVTSLGPRLL LSNNPVQNNE LKTL REILN EFPDSERDKW SVSINVFEVY LKLVLDNVET QETIDSLISG MKIFYDQYKH CREVAACCNV MSQEIVSKIL EKNNP SIGD SKAKLLELPL GQPEKAYLRG EFAQDLMKCT YKI

UniProtKB: NUP145 isoform 1

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Macromolecule #4: Protein transport protein SEC13

MacromoleculeName: Protein transport protein SEC13 / type: protein_or_peptide / ID: 4 / Details: cofactor of Nup145C on stem of Nup84 Y-complex / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 33.082965 KDa
SequenceString: MVVIANAHNE LIHDAVLDYY GKRLATCSSD KTIKIFEVEG ETHKLIDTLT GHEGPVWRVD WAHPKFGTIL ASCSYDGKVL IWKEENGRW SQIAVHAVHS ASVNSVQWAP HEYGPLLLVA SSDGKVSVVE FKENGTTSPI IIDAHAIGVN SASWAPATIE E DGEHNGTK ...String:
MVVIANAHNE LIHDAVLDYY GKRLATCSSD KTIKIFEVEG ETHKLIDTLT GHEGPVWRVD WAHPKFGTIL ASCSYDGKVL IWKEENGRW SQIAVHAVHS ASVNSVQWAP HEYGPLLLVA SSDGKVSVVE FKENGTTSPI IIDAHAIGVN SASWAPATIE E DGEHNGTK ESRKFVTGGA DNLVKIWKYN SDAQTYVLES TLEGHSDWVR DVAWSPTVLL RSYLASVSQD RTCIIWTQDN EQ GPWKKTL LKEEKFPDVL WRASWSLSGN VLALSGGDNK VTLWKENLEG KWEPAGEVHQ

UniProtKB: Protein transport protein SEC13

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Macromolecule #5: Nucleoporin Seh1

MacromoleculeName: Nucleoporin Seh1 / type: protein_or_peptide / ID: 5 / Details: cofactor Nup85 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 34.652078 KDa
SequenceString: MQPFDSGHDD LVHDVVYDFY GRHVATCSSD QHIKVFKLDK DTSNWELSDS WRAHDSSIVA IDWASPEYGR IIASASYDKT VKLWEEDPD QEECSGRRWN KLCTLNDSKG SLYSVKFAPA HLGLKLACLG NDGILRLYDA LEPSDLRSWT LTSEMKVLSI P PANHLQSD ...String:
MQPFDSGHDD LVHDVVYDFY GRHVATCSSD QHIKVFKLDK DTSNWELSDS WRAHDSSIVA IDWASPEYGR IIASASYDKT VKLWEEDPD QEECSGRRWN KLCTLNDSKG SLYSVKFAPA HLGLKLACLG NDGILRLYDA LEPSDLRSWT LTSEMKVLSI P PANHLQSD FCLSWCPSRF SPEKLAVSAL EQAIIYQRGK DGKLHVAAKL PGHKSLIRSI SWAPSIGRWY QLIATGCKDG RI RIFKITE KNLQVELLSE HDDHNGEVWS VSWNLTGTIL SSAGDDGKVR LWKATYSNEF KCMSVITAQQ

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Macromolecule #6: Nucleoporin NUP84

MacromoleculeName: Nucleoporin NUP84 / type: protein_or_peptide / ID: 6 / Details: tail of Nup84 Y-complex / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 83.718867 KDa
SequenceString: MELSPTYQTE RFTKFSDTLK EFKIEQNNEQ NPIDPFNIIR EFRSAAGQLA LDLANSGDES NVISSKDWEL EARFWHLVEL LLVFRNADL DLDEMELHPY NSRGLFEKKL MQDNKQLYQI WIVMVWLKEN TYVMERPKNV PTSKWLNSIT SGGLKSCDLD F PLRENTNV ...String:
MELSPTYQTE RFTKFSDTLK EFKIEQNNEQ NPIDPFNIIR EFRSAAGQLA LDLANSGDES NVISSKDWEL EARFWHLVEL LLVFRNADL DLDEMELHPY NSRGLFEKKL MQDNKQLYQI WIVMVWLKEN TYVMERPKNV PTSKWLNSIT SGGLKSCDLD F PLRENTNV LDVKDKEEDH IFFKYIYELI LAGAIDEALE EAKLSDNISI CMILCGIQEY LNPVIDTQIA NEFNTQQGIK KH SLWRRTV YSLSQQAGLD PYERAIYSYL SGAIPNQEVL QYSDWESDLH IHLNQILQTE IENYLLENNQ VGTDELILPL PSH ALTVQE VLNRVASRHP SESEHPIRVL MASVILDSLP SVIHSSVEML LDVVKGTEAS NDIIDKPYLL RIVTHLAICL DIIN PGSVE EVDKSKLITT YISLLKLQGL YENIPIYATF LNESDCLEAC SFILSSLEDP QVRKKQIETI NFLRLPASNI LRRTT QRVF DETEQEYSPS NEISISFDVN NIDMHLIYGV EWLIEGKLYV DAVHSIIALS RRFLLNGRVK ALEQFMERNN IGEICK NYE LEKIADNISK DENEDQFLEE ITQYEHLIKG IREYEEWQKS VSLLSSESNI PTLIEKLQGF SKDTFELIKT FLVDLTS SN FADSADYEIL YEIRALYTPF LLMELHKKLV EAAKLLKIPK FISEALAFTS LVANENDKIY LLFQSSGKLK EYLDLVAR T ATLSN

UniProtKB: Nucleoporin NUP84

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Macromolecule #7: NUP133 isoform 1

MacromoleculeName: NUP133 isoform 1 / type: protein_or_peptide / ID: 7 / Details: tail Nup84 Y-complex / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 133.452672 KDa
SequenceString: MSEKKVHLRL RKELSVPIAV VENESLAQLS YEEESQASLM DISMEQQQLR LHSHFDNSKV FTENNRYIVK TLQTDYSSGF SNDDELNGY IDMQIGYGLV NDHKKVYIWN IHSTQKDTPY ITVPFRSDDN DEIAVAPRCI LTFPATMDES PLALNPNDQD E TGGLIIIK ...String:
MSEKKVHLRL RKELSVPIAV VENESLAQLS YEEESQASLM DISMEQQQLR LHSHFDNSKV FTENNRYIVK TLQTDYSSGF SNDDELNGY IDMQIGYGLV NDHKKVYIWN IHSTQKDTPY ITVPFRSDDN DEIAVAPRCI LTFPATMDES PLALNPNDQD E TGGLIIIK GSKAIYYEDI NSINNLNFKL SEKFSHELEL PINSSGGEKC DLMLNCEPAG IVLSTNMGRI FFITIRNSMG KP QLKLGKL LNKPFKLGIW SKIFNTNSSV VSLRNGPILG KGTRLVYITT NKGIFQTWQL SATNSHPTKL IDVNIYEAIL ESL QDLYPF AHGTLKIWDS HPLQDESSQL FLSSIYDSSC NETYYILSTI IFDSSSNSFT IFSTYRLNTF MESITDTKFK PKIF IPQME NANDTNEVTS ILVMFPNAVV ITQVNSKLDS SYSMRRKWED IVSLRNDIDI IGSGYDSKSL YVLTKQMGVL QFFVK ENEE TNSKPEVGFV KSHVDQAVYF SKINANPIDF NLPPEISLDQ ESIEHDLKLT SEEIFHSNGK YIPPMLNTLG QHLSVR KEF FQNFLTFVAK NFNYKISPEL KLDLIEKFEI LNCCIKFNSI IRQSDVLNDI WEKTLSNYNL TQNEHLTTKT VVINSPD VF PVIFKQFLNH VVFVLFPSQN QNFKLNVTNL INLCFYDGIL EEGEKTIRYE LLELDPMEVD TSKLPWFINF DYLNCINQ C FFDFTFACEE EGSLDSYKEG LLKIVKILYY QFNQFKIWIN TQPVKSVNAN DNFININNLY DDNHLDWNHV LCKVNLKEQ CIQIAEFYKD LSGLVQTLQT LDQNDSTTVS LYETFFNEFP KEFSFTLFEY LIKHKKLNDL IFRFPQQHDV LIQFFQESAP KYGHVAWIQ QILDGSYADA MNTLKNITVD DSKKGESLSE CELHLNVAKL SSLLVEKDNL DINTLRKIQY NLDTIDAEKN I SNKLKKGE VQICKRFKNG SIREVFNILV EELKSTTVVN LSDLVELYSM LDDEESLFIP LRLLSVDGNL LNFEVKKFLN AL VWRRIVL LNASNEGDKL LQHIVKRVFD EELPKNNDFP LPSVDLLCDK SLLTPEYISE TYGRFPIDQN AIREEIYEEI SQV ETLNSD NSLEIKLHST IGSVAKEKNY TINYETNTVE Y

UniProtKB: NUP133 isoform 1

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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

Concentration0.1 mg/mL
BufferpH: 7.5
Details: 20mM HEPES,50mM Potassium acetate,20mM NaCl,2mM MgCl2,1mM DTT
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK III
DetailsOne step affinity purified

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated magnification: 37651 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
DetailsPreliminary grid screening done manually with individual images of low magnification montages of candidate meshes.
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 2-40 / Number grids imaged: 1 / Number real images: 4015 / Average electron dose: 40.0 e/Å2 / Details: 3218 images retained after triage
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 26049
Startup modelType of model: OTHER
Details: 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.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.7)
Details: C8 symmetry used followed by Multibody processing focused on a double Y-complex protomer
Final 3D classificationSoftware - Name: RELION (ver. 3.0.7)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2) / Software - details: non-uniform refinement
Details: C1 symmetry used to refine to refine double Y-complex protomer
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 8.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Software - details: non-uniform refinement
Details: multibody in RELION followed by refinements in cryosparc
Number images used: 29655
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model / Details: none
DetailsMolecular dynamics flexible fitting after docking Alphafold2 CSMs for Nups into the 3D map of double Y complex ring with Chimera
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: cross correlation
Output model

PDB-8tie:
Double nuclear outer ring of Nup84-complexes from the yeast NPC

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