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- EMDB-32658: Cryo-EM structure of the inner ring monomer of the Saccharomyces ... -

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Basic information

Entry
Database: EMDB / ID: EMD-32658
TitleCryo-EM structure of the inner ring monomer of the Saccharomyces cerevisiae nuclear pore complex
Map data
Sample
  • Complex: Cryo-EM structure of the inner ring monomer of the Saccharomyces cerevisiae nuclear pore complex
    • Protein or peptide: Nucleoporin NUP188
  • Protein or peptide: Nucleoporin NIC96
  • Protein or peptide: Nucleoporin NUP157
  • Protein or peptide: Nucleoporin NUP170
  • Protein or peptide: Nucleoporin NUP192
  • Protein or peptide: Nucleoporin NUP49/NSP49
  • Protein or peptide: Nucleoporin NUP57
  • Protein or peptide: Nucleoporin NSP1
Keywordsnuclear pore complex / inner ring / monomer / Saccharomyces cerevisiae / TRANSPORT PROTEIN
Function / homology
Function and homology information


nuclear pore linkers / mRNA export from nucleus in response to heat stress / nuclear pore inner ring / protein localization to nuclear inner membrane / chromosome, subtelomeric region / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore central transport channel / regulation of nucleocytoplasmic transport / nuclear pore organization / nuclear pore complex assembly ...nuclear pore linkers / mRNA export from nucleus in response to heat stress / nuclear pore inner ring / protein localization to nuclear inner membrane / chromosome, subtelomeric region / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore central transport channel / regulation of nucleocytoplasmic transport / nuclear pore organization / nuclear pore complex assembly / telomere tethering at nuclear periphery / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / nuclear pore nuclear basket / tRNA export from nucleus / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / RNA export from nucleus / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / NLS-bearing protein import into nucleus / ribosomal large subunit export from nucleus / mRNA transport / nuclear pore / ribosomal small subunit export from nucleus / nuclear periphery / chromosome segregation / promoter-specific chromatin binding / molecular condensate scaffold activity / heterochromatin formation / phospholipid binding / protein import into nucleus / protein transport / nuclear envelope / nuclear membrane / amyloid fibril formation / chromatin binding / protein-containing complex binding / DNA binding / RNA binding / identical protein binding / nucleus
Similarity search - Function
Nuclear pore protein Nup188, C-terminal / Nuclear pore protein NUP188 C-terminal domain / Nucleoporin Nup188, N-terminal / Nucleoporin Nup188, N-terminal / Nucleoporin Nup54/Nup57/Nup44 / Nucleoporin p58/p45 / Nucleoporin Nup54, alpha-helical domain / Nucleoporin Nup188 / : / Nucleoporin complex subunit 54 ...Nuclear pore protein Nup188, C-terminal / Nuclear pore protein NUP188 C-terminal domain / Nucleoporin Nup188, N-terminal / Nucleoporin Nup188, N-terminal / Nucleoporin Nup54/Nup57/Nup44 / Nucleoporin p58/p45 / Nucleoporin Nup54, alpha-helical domain / Nucleoporin Nup188 / : / Nucleoporin complex subunit 54 / Nucleoporin Nup188, N-terminal subdomain III / Nucleoporin, NSP1-like, C-terminal / Nucleoporin NSP1/NUP62 / Nsp1-like C-terminal region / Nucleoporin, Nup155-like / Nucleoporin, Nup155-like, C-terminal, subdomain 1 / Nucleoporin, Nup155-like, C-terminal, subdomain 2 / Nucleoporin Nup186/Nup192/Nup205 / Nuclear pore complex scaffold, nucleoporins 186/192/205 / Nucleoporin, Nup133/Nup155-like, C-terminal / Non-repetitive/WGA-negative nucleoporin C-terminal / Nucleoporin interacting component Nup93/Nic96 / Nup93/Nic96 / Nucleoporin FG repeat / Nucleoporin FG repeat region / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like
Similarity search - Domain/homology
Nucleoporin NSP1 / Nucleoporin NIC96 / Nucleoporin NUP170 / Nucleoporin NUP157 / Nucleoporin NUP192 / Nucleoporin NUP57 / Nucleoporin NUP188 / Nucleoporin NUP49/NSP49
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.73 Å
AuthorsLi ZQ / Chen SJB / Zhao L / Sui SF
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Res / Year: 2022
Title: Near-atomic structure of the inner ring of the Saccharomyces cerevisiae nuclear pore complex.
Authors: Zongqiang Li / Shuaijiabin Chen / Liang Zhao / Guoqiang Huang / Xiong Pi / Shan Sun / Peiyi Wang / Sen-Fang Sui /
Abstract: Nuclear pore complexes (NPCs) mediate bidirectional nucleocytoplasmic transport of substances in eukaryotic cells. However, the accurate molecular arrangement of NPCs remains enigmatic owing to their ...Nuclear pore complexes (NPCs) mediate bidirectional nucleocytoplasmic transport of substances in eukaryotic cells. However, the accurate molecular arrangement of NPCs remains enigmatic owing to their huge size and highly dynamic nature. Here we determined the structure of the asymmetric unit of the inner ring (IR monomer) at 3.73 Å resolution by single-particle cryo-electron microscopy, and created an atomic model of the intact IR consisting of 192 molecules of 8 nucleoporins. In each IR monomer, the Z-shaped Nup188-Nup192 complex in the middle layer is sandwiched by two approximately parallel rhomboidal structures in the inner and outer layers, while Nup188, Nup192 and Nic96 link all subunits to constitute a relatively stable IR monomer. In contrast, the intact IR is assembled by loose and instable interactions between IR monomers. These structures, together with previously reported structural information of IR, reveal two distinct interaction modes between IR monomers and extensive flexible connections in IR assembly, providing a structural basis for the stability and malleability of IR.
History
DepositionJan 22, 2022-
Header (metadata) releaseApr 13, 2022-
Map releaseApr 13, 2022-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32658.png

Downloads & links

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Map

FileDownload / File: emd_32658.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 350 pix.
= 467.6 Å		1.34 Å/pix.
x 350 pix.
= 467.6 Å		1.34 Å/pix.
x 350 pix.
= 467.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.336 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-1.4494749 - 2.4826643
Average (Standard dev.)0.0058103045 (±0.04833225)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 467.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of the inner ring monomer of the Saccharomyces ...

EntireName: Cryo-EM structure of the inner ring monomer of the Saccharomyces cerevisiae nuclear pore complex
Components
  • Complex: Cryo-EM structure of the inner ring monomer of the Saccharomyces cerevisiae nuclear pore complex
    • Protein or peptide: Nucleoporin NUP188
  • Protein or peptide: Nucleoporin NIC96
  • Protein or peptide: Nucleoporin NUP157
  • Protein or peptide: Nucleoporin NUP170
  • Protein or peptide: Nucleoporin NUP192
  • Protein or peptide: Nucleoporin NUP49/NSP49
  • Protein or peptide: Nucleoporin NUP57
  • Protein or peptide: Nucleoporin NSP1

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Supramolecule #1: Cryo-EM structure of the inner ring monomer of the Saccharomyces ...

SupramoleculeName: Cryo-EM structure of the inner ring monomer of the Saccharomyces cerevisiae nuclear pore complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #4
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Nucleoporin NIC96

MacromoleculeName: Nucleoporin NIC96 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 96.291586 KDa
SequenceString: MLETLRGNKL HSGTSKGANK KLNELLESSD NLPSASSELG SIQVSINELR RRVFQLRSKN KASKDYTKAH YLLANSGLSF EDVDAFIKD LQTNQFLEPN PPKIIESEEL EFYIRTKKEE NILMSIEQLL NGATKDFDNF INHNLNLDWA QHKNEVMKNF G ILIQDKKT ...String:
MLETLRGNKL HSGTSKGANK KLNELLESSD NLPSASSELG SIQVSINELR RRVFQLRSKN KASKDYTKAH YLLANSGLSF EDVDAFIKD LQTNQFLEPN PPKIIESEEL EFYIRTKKEE NILMSIEQLL NGATKDFDNF INHNLNLDWA QHKNEVMKNF G ILIQDKKT VDHKKSISSL DPKLPSWGNK GNNILNSNES RLNVNENNIL REKFENYARI VFQFNNSRQA NGNFDIANEF IS ILSSANG TRNAQLLESW KILESMKSKD INIVEVGKQY LEQQFLQYTD NLYKKNMNEG LATNVNKIKS FIDTKLKKAD KSW KISNLT VINGVPIWAL IFYLLRAGLI KEALQVLVEN KANIKKVEQS FLTYFKAYAS SKDHGLPVEY STKLHTEYNQ HIKS SLDGD PYRLAVYKLI GRCDLSRKNI PAVTLSIEDW LWMHLMLIKE KDAENDPVYE RYSLEDFQNI IISYGPSRFS NYYLQ TLLL SGLYGLAIDY TYTFSEMDAV HLAIGLASLK LFKIDSSTRL TKKPKRDIRF ANILANYTKS FRYSDPRVAV EYLVLI TLN EGPTDVELCH EALRELVLET KEFTVLLGKI GRDGARIPGV IEERQPLLHV RDEKEFLHTI TEQAARRADE DGRIYDS IL LYQLAEEYDI VITLVNSLLS DTLSASDLDQ PLVGPDDNSE TNPVLLARRM ASIYFDNAGI SRQIHVKNKE ICMLLLNI S SIRELYFNKQ WQETLSQMEL LDLLPFSDEL SARKKAQDFS NLDDNIVKNI PNLLIITLSC ISNMIHILNE SKYQSSTKG QQIDSLKNVA RQCMIYAGMI QYRMPRETYS TLINIDVSL

UniProtKB: Nucleoporin NIC96

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Macromolecule #2: Nucleoporin NUP157

MacromoleculeName: Nucleoporin NUP157 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 156.827484 KDa
SequenceString: MYSTPLKKRI DYDRETFTAS ASLGGNRLRN RPRDDQNNGK PNLSSRSFLS ERKTRKDVLN KYGEAGNTIE SELRDVTTHV KISGLTSSE PLQLASEFVQ DLSFRDRNTP ILDNPDYYSK GLDYNFSDEV GGLGAFTPFQ RQQVTNIPDE VLSQVSNTEI K SDMGIFLE ...String:
MYSTPLKKRI DYDRETFTAS ASLGGNRLRN RPRDDQNNGK PNLSSRSFLS ERKTRKDVLN KYGEAGNTIE SELRDVTTHV KISGLTSSE PLQLASEFVQ DLSFRDRNTP ILDNPDYYSK GLDYNFSDEV GGLGAFTPFQ RQQVTNIPDE VLSQVSNTEI K SDMGIFLE LNYCWITSDN KLILWNINNS SEYHCIDEIE HTILKVKLVK PSPNTFVSSV ENLLIVATLF DIYILTISFN DR THELNIF NTGLKVNVTG FNVSNIISYE RTGQIFFTGA TDGVNVWELQ YNCSENLFNS KSNKICLTKS NLANLLPTKL IPS IPGGKL IQKVLEGDAG TEEETISQLE VDQSRGVLHT LSTKSIVRSY LITSNGLVGP VLIDAAHIRR GMNALGVKNS PLLS NRAFK IAKIVSISMC ENNDLFLAVI TTTGVRLYFK GSISRRSIGS LKLDSVKFPP TSISSSLEQN KSFIIGHHPL NTHDT GPLS TQKASSTYIN TTCASTIISP GIYFTCVRKR ANSGELSKGI TNKALLENKE EHKLYVSAPD YGILKNYGKY VENTAL LDT TDEIKEIVPL TRSFNYTSTP QGYANVFASQ YSAEPLKVAV LTSNALEIYC YRTPDEVFES LIENPLPFIH SYGLSEA CS TALYLACKFN KSEHIKSSAL AFFSAGIPGV VEIKPKSSRE SGSVPPISQN LFDKSGECDG IVLSPRFYGS ALLITRLF S QIWEERVFVF KRASKTEKMD AFGISITRPQ VEYYLSSISV LADFFNIHRP SFVSFVPPKG SNAITASDAE SIAMNALIL LINSIKDALS LINVFYEDID AFKSLLNTLM GAGGVYDSKT REYFFDLKFH DLFTPNAKTK QLIKEILIEV VNANIASGTS ADYIVNVLK ERFGSFCHSA DILCYRAGEH LEAAQKFEMI DSKISRNHLD TAIDLYERCA ENIELCELRR VVDIMVKLNY Q PKTVGFLL RFADKIDKGN QAQEYVSRGC NTADPRKVFY DKRINVYTLI FEIVKSVDDY TSIEQSPSIA NISIFSPASS LK KRVYSVI MNSNNRFFHY CFYDWLVANK RQDYLLRLDS QFVLPYLKER AEKSLEISNL LWFYLFKEEH FLEAADVLYA LAS SDFDLK LSERIECLAR ANGLCDSSTS FDQKPALVQL SENIHELFDI ASIQDDLLNL VRNETRIDED YRKQLTLKLN GRVL PLSDL FNDCADPLDY YEIKLRIFKV SQFKDEKVIQ GEWNRLLDSM KNAPSPDVGS VGQESFLSSI SNTLIRIGKT TRDTD VVFP VHFLMNKILE SFIDKSSAAD GSVCSMFLLA GVSHLKLYYI LSRIIENSEG NVELAKKEMV WLIKDWYQSD SDLRGS IAP EQIKKLEKYD PNTDPVQDYV KDRHHGLK

UniProtKB: Nucleoporin NUP157

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Macromolecule #3: Nucleoporin NUP170

MacromoleculeName: Nucleoporin NUP170 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 169.651969 KDa
SequenceString: MFQSFFHNNG PAAAGETFSD SRSYPLTNHQ EVPRNGLNEL ASSATKAQQQ PTHILNSYPI TGSNPLMRAS AMGATSGSIN PNMSNMNEH IRVSGMGTSK PLDLAGKYID HLQHKDSNTP VLDERSYYNS GVDYNFSREK NGLGAFTPFE KQDVFNIPDE I LHEFSTSQ ...String:
MFQSFFHNNG PAAAGETFSD SRSYPLTNHQ EVPRNGLNEL ASSATKAQQQ PTHILNSYPI TGSNPLMRAS AMGATSGSIN PNMSNMNEH IRVSGMGTSK PLDLAGKYID HLQHKDSNTP VLDERSYYNS GVDYNFSREK NGLGAFTPFE KQDVFNIPDE I LHEFSTSQ TKTDMGIFPE LNRCWITIDN KLILWNINND NEYQVVDDMK HTIQKVALVR PKPNTFVPAV KHLLLISTTM EL FMFAISL DKATNELSVF NTHLSVPVQG IDVIDIVSHE RSGRIFFAGQ ASGLNIWELH YSGSDDWFNS KCSKVCLTKS ALL SLLPTN MLSQIPGVDF IQALFEDNSN GNGGFSQETI TQLTIDQQRG IIYSLSSKST IRAYVITEKS LEGPMSIEPA YISR IIGTT TARAAPILGP KYLKIVKISS VAPEENNNLF LVALTVGGVR LYFNGSMGRF NIEALRLESI KFPPSSVTPE VIQQE LLHQ QQEQAKRSFP FFSNLMSSEP VLLKFQKKSS VLLETTKAST IISPGIFFSA VIKSSQQTHQ QEKKENSSVT GTTATA GSK TVKQQPVTLQ HKLFVSVPDY GILKTHGKYV ENATFLETAG PVQQIIPLSG LFNATTKPQG FANEFATQYT SETLRVA VL TSTSIEIYKY RTPDEIFEDL IDNPLPFVLN YGAAEACSTA LFVTCKSNKS EKLRSNALTF LTMGIPGVVD IKPVYNRY S VSTVSSLLSK PTLSTATTNL QQSITGFSKP SPANKEDFDL DDVILSPRFY GIALLITRLL RDIWGRHVFM TFTDNRVTS HAFISSSDPI TPSINNLKSD EISQNRNIIS KVSISKDCIE YYLSSINILN EFFITYGDSI SQISAPYVLA NNSNGRVIDK TEEVANQAE SIAINAMIKM VQSIKEGLSF LNVLYEESEV EGFDNQYLGF KDIISFVSLD VQKDLVKLDF KDLFAPNDKT K SLIREILL SIINRNITKG ASIEYTATAL QERCGSFCSA SDILGFRAIE HLRRAKEIGL RNYDSLNYHL KNATALLEQI VD DLSIEKL KEAVSMMLSV NYYPKSIEFL LNIANSMDKG KLACQYVANG FLENDDRKQY YDKRILVYDL VFDTLIKVDE LAE KKQSSK TQNQISISND DEVKLRQKSY EAALKYNDRL FHYHMYDWLV SQNREEKLLD IETPFILPYL MEKAGSSLKI SNIL WVYYS RRSKFFESAE ILYRLATSNF DITLFERIEF LSRANGFCNS VSPLSQKQRI VQLASRIQDA CEVAGIQGDI LSLVY TDAR IDSAIKDELI KTLDGKILST SELFNDFAVP LSYHEIALFI FKIADFRDHE VIMAKWDELF QSLRMEFNNT GKKEDS MNF INLLSNVLIK IGKNVQDSEF IFPIFELFPI VCNFFYETLP KEHIVSGSIV SIFITAGVSF NKMYYILKEL IETSDSD NS VFNKEMTWLI HEWYKSDRKF RDIISYNDII HLKEYKIDND PIEKYVKNSG NNLGICFYKE

UniProtKB: Nucleoporin NUP170

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Macromolecule #4: Nucleoporin NUP188

MacromoleculeName: Nucleoporin NUP188 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 188.753281 KDa
SequenceString: MATPSFGNSS PQLTFTHVAN FMNDAAADVS AVDAKQLAQI RQFLKANKTN LIESLNTIRQ NVTSSGDHNK LRSTIANLLQ INVDNDPFF AQSEDLSHAV EFFMSERSSR LHIVYSLLVN PDIDLETYSF IDNDRFNVVG KLISIISSVI QNYDIITASS L AHDYNNDQ ...String:
MATPSFGNSS PQLTFTHVAN FMNDAAADVS AVDAKQLAQI RQFLKANKTN LIESLNTIRQ NVTSSGDHNK LRSTIANLLQ INVDNDPFF AQSEDLSHAV EFFMSERSSR LHIVYSLLVN PDIDLETYSF IDNDRFNVVG KLISIISSVI QNYDIITASS L AHDYNNDQ DMFTIVSLVQ LKKFSDLKFI LQILQILNLM ILNTKVPVDI VNQWFLQYQN QFVEFCRNIN STDKSIDTSS LQ LYKFQNF QDLSYLSETL ISRISSLFTI TTILILGLNT SIAQFDIQSP LYMDTETFDT VNSALENDVA TNIVNEDPIF HPM IHYSWS FILYYRRALQ SSESFDDSDI TKFALFAESH DVLQKLNTLS EILSFDPVYT TVITVFLEFS LNFIPITAST SRVF AKIIS KAPEQFIENF LTNDTFEKKL SIIKAKLPLL NESLIPLINL ALIDTEFANF ELKDICSFAV TKSSLNDLDY DLIAD TITN SSSSSDIIVP DLIELKSDLL VAPPLENENS NCLLSIPKST KGKILTIKQQ QQQQQQQNGQ QPPTTSNLII FLYKFN GWS LVGRILQNLL HSYMEKGTQL DDLQHELMIS IIKLVTNVVD PKTSIEKSSE ILSYLSNSLD TSASTINGAS IIQVIFE IF EISLQRKDYT SIVQCCEFMT MLTPNYLHLV SSYLNKSDLL DKYGKTGLSN MILGSVELST GDYTFTIQLL KLTKVFIR E SLSLKNIHIS KRSKIDIINK LILHAIHIFE SYYNWKYNNF LQKFEIAFHL TLIFYDVLHD VFTINPHQKD QLIISSSAN KLLQLFLTPM DSIDLAPNTL TNILISPLNT TTKILGDKIL GNLYSKVMNN SFKLCTLLIA IRGSNRDLKP SNLEKLLFIN SSKLVDVYT LPSYVHFKVQ IIELLSYLVE APWNDDYPFL LSFLGEAKSM AFLKEVLSDL SSPVQDWNLL RSLYIFFTTL L ESKQDGLS ILFLTGQFAS NKKINDESSI DKKSSILTVL QKNSLLLDST PEEVSCKLLE TITYVLNTWT NSKIFIKDPK FV NSLLAKL KDSKKLFQKK ENLTRDETVS LIKKYKLISR IVEIFALCIY NSTDSNSEIL NFLNQEDLFE LVHHFFQIDG FNK TFHDEL NLKFKEKWPS LELQSFQKIP LSRINENENF GYDIPLLDIV LKADRSWNEP SKSQTNFKEE ITDASLNLQY VNYE ISTAK AWGALITTFV KRSTVPLNDG FVDLVEHFLK LNIDFGSDKQ MFTQIYLERI ELSFYILYSF KLSGKLLKEE KIIEL MNKI FTIFKSGEID FIKNIGKSLK NNFYRPLLRS VLVLLELVSS GDRFIELISD QLLEFFELVF SKGVYLILSE ILCQIN KCS TRGLSTDHTT QIVNLEDNTQ DLLLLLSLFK KITNVNPSKN FNVILASSLN EVGTLKVILN LYSSAHLIRI NDEPILG QI TLTFISELCS IEPIAAKLIN SGLYSVLLES PLSVAIQQGD IKPEFSPRLH NIWSNGLLSI VLLLLSQFGI KVLPETCL F VSYFGKQIKS TIYNWGDNKL AVSSSLIKET NQLVLLQKML NLLNYQELFI QPKNSDDQQE AVELVIGLDS EHDKKRLSA ALSKFLTHPK YLNSRIIPTT LEEQQQLEDE SSRLEFVKGI SRDIKALQDS LFKDV

UniProtKB: Nucleoporin NUP188

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Macromolecule #5: Nucleoporin NUP192

MacromoleculeName: Nucleoporin NUP192 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 191.718125 KDa
SequenceString: MKWSAIPFQT LYRSIESGEF DFDLFKEVLP DLQNLNLNTD KLKNNASRSQ LEKGEIELSD GSTFKVNQEF IFEAISLSDE LNLDEIVAC ELILSGDTTA NNGKVQYFLR RQYILQIVSF IVNCFHEDTE LYQELIKNGA LVSNILSAFK FIHTQLSEIK Q QINKAQIL ...String:
MKWSAIPFQT LYRSIESGEF DFDLFKEVLP DLQNLNLNTD KLKNNASRSQ LEKGEIELSD GSTFKVNQEF IFEAISLSDE LNLDEIVAC ELILSGDTTA NNGKVQYFLR RQYILQIVSF IVNCFHEDTE LYQELIKNGA LVSNILSAFK FIHTQLSEIK Q QINKAQIL ENYNALFQQN IKFRRDFLLR EYDILSQILY GLVDKGAIMK NKDFILSLLH HVSELDSNDF FIIYYTPAFF HL FASLRVL PDADVKLLHS QFMKDLKDDS IYTKPVKVAL IFIFFAYFIG WCKEDPKRRA DTMDFKTDVD EPMTSAVELG AIE QILIFA ADTSIVEQDK SMELFYDIRS LLERHIPRLI PKQLLDDEKI FSQTTNSTYN PASATDNMSG RGLWNPSYPG MMST TGTAR LNSMPNNVNE YSYTTIVLSD QTQEFFLSSF DDVLQTIITD CAFLLTKIKD AEEDSLLSGE DLTLDDISLK ADLER FFLS IYFFYASRPE YSCTFWSDKE SNAYGFIEWC SRCNDNLMRS CFYLMVSSLS FGPENALNVY HYFGENSSIS WKNIAQ CLS DYTKKISNFN SSLHKRQQFS ESTHNDIDST AVALEEGLNE EAVIFLSSLL TLVGSVTYQV DEDVKSSLSK VFSDVLF EF TKINTPLVGA AFKVISNLVP KLESSRTKFW SFLDSLIFKD SSLNYSSESY RNAFTNVLTK YSDVLGFLQL FHNLISIH S RENNSEYMVF GKLAFPTRLG QGYRKVGIWP YFDYIFNDIL AHVDQIVDIR NKRAVQLPIL KIIYTGLCSF DYSVILNSI PAAANLDALV DCENFFNYVQ ECPAIPIFNY IFTEKIYKSI FNVVDVGVDQ LSIELEGGKN QAELLQLAVK IINKVLDYQE TYVEELFPI VKKHGKTDYF LPKNYSLHGL RSFYDAIFFN IPLVAHLGLY VGVDDQILAT NSLRILAKLS ERSNGSVASL S KRNKLLTI FDSVDESARI KDAFITQLES SITDAGVLAL KLELLDFLTS NLSNYSRTMT ISHLLLGFQV SNVISLGPNL AT FISSGTS LLDSLISVLE ASLNSITKDN IDYAPMRLAT AALEIILKLC RNPLTSGLLY SYLIKENFFE RIMILDPQVT RFT TWNGSP FDNSTEEKCK NFIESESVGA FLSFLAYRNY WTQYLGLFIH KISFSGTKSE VLTYVNYLIS NTMYSVRLFS FLDP LNYGN ICEPKETLSI FTNVPLNLEQ VTLNKYCSGN IYDFHKMENL MRLIKRVRAE SLHSNSFSLT VSKEQFLKDA DVECI KAKS HFTNIISRNK ALELNLSVLH SWVQLVQIIV TDGKLEPSTR SNFILEVFGT IIPKISDYIE FNITFSEELV SLAVFL FDI YNRDRKLITD KGTVDGRLYQ LFKTCIQGIN SPLSSVALRS DFYILANHYL SRVLSDQVGS EKVLQDLRLG SKKLVEI IW NDVVYGEGTS RVTGILLLDS LIQLANRSKE NFILDSLMKT TRLLLIIRSL KNTDALLNST TEHINIDDLL YELTAFKA T VFFLIRVAET RGGASALIEN NLFRIIAELS FLKVDPDLGL DLMFDEVYVQ NSKFLKVNVT LDNPLLVDKD ANGVSLFEL IVPIFQLISA VLVSMGSSNK AVVQTVKGLL NTYKRLVIGI FKRDLLREKE DKKNSSDPNN QSLNEMVKLI VMLCTLTGYQ NND

UniProtKB: Nucleoporin NUP192

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Macromolecule #6: Nucleoporin NUP49/NSP49

MacromoleculeName: Nucleoporin NUP49/NSP49 / type: protein_or_peptide / ID: 6 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 49.174762 KDa
SequenceString: MFGLNKASST PAGGLFGQAS GASTGNANTG FSFGGTQTGQ NTGPSTGGLF GAKPAGSTGG LGASFGQQQQ QSQTNAFGGS ATTGGGLFG NKPNNTANTG GGLFGANSNS NSGSLFGSNN AQTSRGLFGN NNTNNINNSS SGMNNASAGL FGSKPAGGTS L FGNTSTSS ...String:
MFGLNKASST PAGGLFGQAS GASTGNANTG FSFGGTQTGQ NTGPSTGGLF GAKPAGSTGG LGASFGQQQQ QSQTNAFGGS ATTGGGLFG NKPNNTANTG GGLFGANSNS NSGSLFGSNN AQTSRGLFGN NNTNNINNSS SGMNNASAGL FGSKPAGGTS L FGNTSTSS APAQNQGMFG AKPAGTSLFG NNAGNTTTGG GLFGSKPTGA TSLFGSSNNN NNNNNSNNIM SASGGLFGNQ QQ QLQQQPQ MQCALQNLSQ LPITPMTRIS ELPPQIRQEI EQLDQYIQKQ VQISHHLKAD TIDHDELIDS IPRDVAYLLK SES ATSQYL KQDLKKISSF KSLIDEDLLD TQTFSVLLQQ LLTPGSKISS NDLDKFFQKK IHLYEKKLED YCRILSDIET AVNG IDTDL FGAPNNPNST AITADLGSSE AENLLQLKTG LAAIVSTVIE EFTLFMDIAE RIAVLHQKTK TLASLSI

UniProtKB: Nucleoporin NUP49/NSP49

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Macromolecule #7: Nucleoporin NUP57

MacromoleculeName: Nucleoporin NUP57 / type: protein_or_peptide / ID: 7 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 57.547145 KDa
SequenceString: MFGFSGSNNG FGNKPAGSTG FSFGQNNNNT NTQPSASGFG FGGSQPNSGT ATTGGFGANQ ATNTFGSNQQ SSTGGGLFGN KPALGSLGS SSTTASGTTA TGTGLFGQQT AQPQQSTIGG GLFGNKPTTT TGGLFGNSAQ NNSTTSGGLF GNKVGSTGSL M GGNSTQNT ...String:
MFGFSGSNNG FGNKPAGSTG FSFGQNNNNT NTQPSASGFG FGGSQPNSGT ATTGGFGANQ ATNTFGSNQQ SSTGGGLFGN KPALGSLGS SSTTASGTTA TGTGLFGQQT AQPQQSTIGG GLFGNKPTTT TGGLFGNSAQ NNSTTSGGLF GNKVGSTGSL M GGNSTQNT SNMNAGGLFG AKPQNTTATT GGLFGSKPQG STTNGGLFGS GTQNNNTLGG GGLFGQSQQP QTNTAPGLGN TV STQPSFA WSKPSTGSNL QQQQQQQIQV PLQQTQAIAQ QQQLSNYPQQ IQEQVLKCKE SWDPNTTKTK LRAFVYNKVN ETE AILYTK PGHVLQEEWD QAMEKKPSPQ TIPIQIYGFE GLNQRNQVQT ENVAQARIIL NHILEKSTQL QQKHELDTAS RILK AQSRN VEIEKRILKL GTQLATLKNR GLPLGIAEEK MWSQFQTLLQ RSEDPAGLGK TNELWARLAI LKERAKNISS QLDSK LMVF NDDTKNQDSM SKGTGEESND RINKIVEILT NQQRGITYLN EVLEKDAAIV KKYKNKT

UniProtKB: Nucleoporin NUP57

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Macromolecule #8: Nucleoporin NSP1

MacromoleculeName: Nucleoporin NSP1 / type: protein_or_peptide / ID: 8 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 86.611672 KDa
SequenceString: MNFNTPQQNK TPFSFGTANN NSNTTNQNSS TGAGAFGTGQ STFGFNNSAP NNTNNANSSI TPAFGSNNTG NTAFGNSNPT SNVFGSNNS TTNTFGSNSA GTSLFGSSSA QQTKSNGTAG GNTFGSSSLF NNSTNSNTTK PAFGGLNFGG GNNTTPSSTG N ANTSNNLF ...String:
MNFNTPQQNK TPFSFGTANN NSNTTNQNSS TGAGAFGTGQ STFGFNNSAP NNTNNANSSI TPAFGSNNTG NTAFGNSNPT SNVFGSNNS TTNTFGSNSA GTSLFGSSSA QQTKSNGTAG GNTFGSSSLF NNSTNSNTTK PAFGGLNFGG GNNTTPSSTG N ANTSNNLF GATANANKPA FSFGATTNDD KKTEPDKPAF SFNSSVGNKT DAQAPTTGFS FGSQLGGNKT VNEAAKPSLS FG SGSAGAN PAGASQPEPT TNEPAKPALS FGTATSDNKT TNTTPSFSFG AKSDENKAGA TSKPAFSFGA KPEEKKDDNS SKP AFSFGA KSNEDKQDGT AKPAFSFGAK PAEKNNNETS KPAFSFGAKS DEKKDGDASK PAFSFGAKPD ENKASATSKP AFSF GAKPE EKKDDNSSKP AFSFGAKSNE DKQDGTAKPA FSFGAKPAEK NNNETSKPAF SFGAKSDEKK DGDASKPAFS FGAKS DEKK DSDSSKPAFS FGTKSNEKKD SGSSKPAFSF GAKPDEKKND EVSKPAFSFG AKANEKKESD ESKSAFSFGS KPTGKE EGD GAKAAISFGA KPEEQKSSDT SKPAFTFGAQ KDNEKKTEES STGKSTADVK SSDSLKLNSK PVELKPVSLD NKTLDDL VT KWTNQLTESA SHFEQYTKKI NSWDQVLVKG GEQISQLYSD AVMAEHSQNK IDQSLQYIER QQDELENFLD NFETKTEA L LSDVVSTSSG AAANNNDQKR QQAYKTAQTL DENLNSLSSN LSSLIVEINN VSNTFNKTTN IDINNEDENI QLIKILNSH FDALRSLDDN STSLEKQINS IKK

UniProtKB: Nucleoporin NSP1

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 633134
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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