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- EMDB-32566: Cryo-EM structure of the IR subunit from X. laevis NPC -

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Basic information

Entry
Database: EMDB / ID: EMD-32566
TitleCryo-EM structure of the IR subunit from X. laevis NPC
Map dataThe IR subunit
Sample
  • Complex: The IR subunit
    • Protein or peptide: MGC83295 protein
    • Protein or peptide: Nup188 domain-containing protein
    • Protein or peptide: Nuclear pore complex protein Nup93
    • Protein or peptide: Nup155-prov protein
    • Protein or peptide: Nup54
    • Protein or peptide: IL4I1 protein
    • Protein or peptide: MGC84997 protein
    • Protein or peptide: Aaas-prov protein
    • Protein or peptide: Nucleoporin NDC1
Keywordsnuclear pore complex / inner ring / Nup205 / Nup93 / Nup188 / Nup155 / NDC1 / Aladin / STRUCTURAL PROTEIN
Function / homology
Function and homology information


nuclear pore complex assembly / structural constituent of nuclear pore / nuclear localization sequence binding / mRNA transport / nuclear pore / nuclear periphery / protein transport / nuclear membrane / cytosol
Similarity search - Function
Nucleoporin protein Ndc1-Nup / Aladin / Nucleoporin protein Ndc1-Nup / Nup188 SH3-like domain / Nucleoporin FG repeated region / Nup54, C-terminal interacting domain / Nup54 C-terminal interacting domain / Nucleoporin Nup188, N-terminal / Nucleoporin Nup188, N-terminal / Nucleoporin, Nup155-like, C-terminal, subdomain 3 ...Nucleoporin protein Ndc1-Nup / Aladin / Nucleoporin protein Ndc1-Nup / Nup188 SH3-like domain / Nucleoporin FG repeated region / Nup54, C-terminal interacting domain / Nup54 C-terminal interacting domain / Nucleoporin Nup188, N-terminal / Nucleoporin Nup188, N-terminal / Nucleoporin, Nup155-like, C-terminal, subdomain 3 / 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, Nup133/Nup155-like, N-terminal / Nup133 N terminal like / Armadillo-type fold / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Nucleoporin NUP188 / Nucleoporin 54kDa S homeolog isoform X2 / MGC84997 protein / MGC83295 protein / Nucleoporin NDC1 / Aaas-prov protein / Nucleoporin 155kDa L homeolog / Nuclear pore complex protein Nup93 / IL4I1 protein
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsHuang G / Zhan X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Res / Year: 2022
Title: Cryo-EM structure of the inner ring from the Xenopus laevis nuclear pore complex.
Authors: Gaoxingyu Huang / Xiechao Zhan / Chao Zeng / Ke Liang / Xuechen Zhu / Yanyu Zhao / Pan Wang / Qifan Wang / Qiang Zhou / Qinghua Tao / Minhao Liu / Jianlin Lei / Chuangye Yan / Yigong Shi /
Abstract: Nuclear pore complex (NPC) mediates nucleocytoplasmic shuttling. Here we present single-particle cryo-electron microscopy structure of the inner ring (IR) subunit from the Xenopus laevis NPC at an ...Nuclear pore complex (NPC) mediates nucleocytoplasmic shuttling. Here we present single-particle cryo-electron microscopy structure of the inner ring (IR) subunit from the Xenopus laevis NPC at an average resolution of 4.2 Å. A homo-dimer of Nup205 resides at the center of the IR subunit, flanked by two molecules of Nup188. Four molecules of Nup93 each places an extended helix into the axial groove of Nup205 or Nup188, together constituting the central scaffold. The channel nucleoporin hetero-trimer of Nup62/58/54 is anchored on the central scaffold. Six Nup155 molecules interact with the central scaffold and together with the NDC1-ALADIN hetero-dimers anchor the IR subunit to the nuclear envelope and to outer rings. The scarce inter-subunit contacts may allow sufficient latitude in conformation and diameter of the IR. Our structure reveals the molecular basis for the IR subunit assembly of a vertebrate NPC.
History
DepositionJan 10, 2022-
Header (metadata) releaseMar 30, 2022-
Map releaseMar 30, 2022-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32566.png

Downloads & links

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Map

FileDownload / File: emd_32566.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe IR subunit
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 512 pix.
= 710.144 Å		1.39 Å/pix.
x 512 pix.
= 710.144 Å		1.39 Å/pix.
x 512 pix.
= 710.144 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.387 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.020478556 - 0.037659567
Average (Standard dev.)-0.0000037852217 (±0.0016204142)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 710.144 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : The IR subunit

EntireName: The IR subunit
Components
  • Complex: The IR subunit
    • Protein or peptide: MGC83295 protein
    • Protein or peptide: Nup188 domain-containing protein
    • Protein or peptide: Nuclear pore complex protein Nup93
    • Protein or peptide: Nup155-prov protein
    • Protein or peptide: Nup54
    • Protein or peptide: IL4I1 protein
    • Protein or peptide: MGC84997 protein
    • Protein or peptide: Aaas-prov protein
    • Protein or peptide: Nucleoporin NDC1

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Supramolecule #1: The IR subunit

SupramoleculeName: The IR subunit / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Macromolecule #1: MGC83295 protein

MacromoleculeName: MGC83295 protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 227.854141 KDa
SequenceString: MAAQLALNSE ASLWGPYREI WQTVLSALIK RQPEAVHSLD IVLKKYKPDF ISLFKNPPKS AQQHERVQKA STEGIPIKGT QRTRILEEQ LIKEAFILSD LYNIGEIAAV ELLLIGEQQQ PTFHGLTRGL VAILLYWDGK SCMAESLLHL IQARKGKTFT L DHSPEVVS ...String:
MAAQLALNSE ASLWGPYREI WQTVLSALIK RQPEAVHSLD IVLKKYKPDF ISLFKNPPKS AQQHERVQKA STEGIPIKGT QRTRILEEQ LIKEAFILSD LYNIGEIAAV ELLLIGEQQQ PTFHGLTRGL VAILLYWDGK SCMAESLLHL IQARKGKTFT L DHSPEVVS MVTRFTDDLM EQGLTNKILT LISQIDVNNE FDKLKKERGL GNKKHRKEVS DLIKECQQSL AHSLYSWSCQ TP LNREDTL LLIGYLEKVT VEGDGSLDKV NLTLLMSLLY CLDVGFLEQG TDDREELMKQ ASMFMDRQYI AAIHNRLQNT QPW KSPGMQ ATVRLAWALA LRGISQFSEV LEFSEADEPM AEIAIGGNVF LFLTEAVVGS ESFCTDEFFI RRIHKLVTDF PTLM PMKVK QLRNRAEEDA RLIQMSMQMG NEPPASLRRD LEHLLLLIGE LYRKDPFHLE LALEYWCPTE PLQSTSLMGS FLGVA HQRP PQRQVLLSKF VRQMSDLLPA TLYLPYLKML RGLASGPQCA HYCFSLLKAN GGSSAENLQA AGGSPVSWDH FFHSLM LYH EHLRRDLPNT DNIHQRHPPL RGITQRELDG LIACLQLTCT IIDWSESARL ALCEHAQWMP VVVILGLLQC SIPPLLK AE LLKTLAAFGK SPEIAASLWQ SLEYTQILQT VRATGLRQGV GIEVELNEIE SRCEEYPLTR AFCQLISTLV ESSFPTNL G AGLRAPGFEP YLQFLRDTVF LRYRTRAYRR AAEKWEVAEA VLDVFYKLLK DYEPQPEDFV DQYVELQGEE RVAFKPPGF SLMHHLLNES PMLELCLSLM EEGVTQLDTY APFPGKKHLE KAVAYCFMLL NLTLQKENRF MDLLRESHLS MIVTPLEQLL QGINPRSKK ADNVVNIARY LCHGNSNAEL AFESAKILCS ISCNSKIQEK IVGDFTQDQN VSQKLMVGFV SCLDSEEAEE L LDSEKEAE DQVKQTNIRY MTKIHILNLL ITSLEMKAPN LAMFLLGYEL KKPVSTTNLQ DSGVLGCPRT CLHSILDILR KG TDVRAGP VAVWDTPHLA ELCYQVIYQL CACADTSGPT MRYLRTSQDF LFSQLQHLPF SVEESEISAM NQMSWLMKTA TIE LRITSL NRQRSHTQRL LHLLLDDMPT RPYSADGEGG MEDESRSLSG FLHFDTTSKV RRKILRILDS IQFSNEIPEP LQLD FFDRS QIEQVIANCE HKNRRGQTVC NVKLLHRVLV AEVNALQGMA AIGQRPLLME EINTILQYVV ERNKLLQCLH AKRHA LESW RQLVEIILTA CPQDLIPTEH RQLIIRDLLQ DLHVKILDDD AAQELMPIVA GAVFTLTAHL SQSVRTELKQ PMTASG LGQ SQYVQMLDGS FAAPPGTENI SAGFASIGDS SLHMILRNLL EFILKTGGGF QRVRAHLYGS LLYYLQIAQR PDEPDTL ES AHKSMWERLT APEDVFSKLQ RDNLSIFESY GTALMEVVCR DACDGHDIGR MLALALLDRI VSVDRQQQWL LYLSNSGY L KVLVDSLAED DVVLRNLLTP QPPLLKALYI YESKMAFLTR VAKSSQGAIE LLRSGVIVRL AQCQVYDMRP ETDPHGVFG MRETPVFIPA PVERYRQILL PALQICQLIL TSSTAQHLQA AGQVLQFLVA HSDTIQAILR SQEGSLGSLQ ELALLTGIIS KAALPGVLN ELDIGLNDGS MMELQGHIGR FQRQCLALLN RFGGSDRLRQ LSLQDDSSRL DGVSKKDDME LAMQQICSNV M EYCQALMI QNSPSFQQTV CLFTPSLKES ASRDGTRQDS QVSILPSWRL PSLGVVIHLL KQSANNFFTY YDIHRQSVGK LQ NVEQLPP DEIKELCQSE MPVGADKIST TQKYGLARRR LVKLINSRAK LLSLCSYIIE TCLYILWRHL EYYLLHCTTS DSQ DPVFSN MTFGNRRFQD TFNTDPNMDP RNLRQNKVSQ QDVDTLLREG ANSFGESLQK RLLDIESLYC KVRSRHSFIQ ALVR RIRGL LRVSRV

UniProtKB: MGC83295 protein

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Macromolecule #2: Nup188 domain-containing protein

MacromoleculeName: Nup188 domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 195.84875 KDa
SequenceString: MAAAGSLYWR TSRELWTILL GRSSMKDGYQ IKAELDRYGD RLLQGLAYYK PPSTRSADKV KANKNLSPAL QELGLRLSKF LALDEEQSV ELLQTYLQYD YRGTQESVKV LPQDERQSQA LMLKMADYYY EERISLLRCV LYILNYFQDD KHPYSAEFSK C VELMEQKE ...String:
MAAAGSLYWR TSRELWTILL GRSSMKDGYQ IKAELDRYGD RLLQGLAYYK PPSTRSADKV KANKNLSPAL QELGLRLSKF LALDEEQSV ELLQTYLQYD YRGTQESVKV LPQDERQSQA LMLKMADYYY EERISLLRCV LYILNYFQDD KHPYSAEFSK C VELMEQKE LFGKYLKQFE SLCREEAPTW ETHGNFMTER QVSRWFVQRL REQAMLLEII FLYFACFAAS PSDLLALTKL FK EQGFGCR LQNHHLVEPS MDPLVERIGY FSILIFLEAL DMDTLMTCSL SDKIEQHPFS SEEQVCKEMD SILVTLGDVP HHG PVLLAW ALLRFTLNPD KVTSAVRKMG STAIQLHLFQ YLTRMLQSLR SGENNCTTST ACLCVYTFLA YVLSTLEEQV SQSQ QDLVE TACQVFAAPN LPDLFWNMEP TAGLGILLDS VVGMFPFRIS PLLKLFTALV SKSSAKKVYS FLDRMSSYTE HYRHK PHDI LSHDDETLWK RQTPKLLYAL GLGQTNLRIP QGALGQVMAD ENGFLVRWEY SYSCWTLFTC EIEMLLHVVS TADVIH QCQ RVKPIIDLVH KVISTDLSIA DCLLPITSRI YMLLQRLTTV MNPPMDFLSS CVDCLTALAT RLPAKVWTDL RHTGFLP FA ANPVSGHLIS TEGMNAGGYG SLFGIEQSQG EYSVTLSFLR LITTLVKGQL GSTQSQGLVP CILFVLREML PNYHRWRY N SHGVREQLGF QILSLIHAIL NLCPEEEEGS SAPNLRSLCI FSLTNTEAGQ AVINIMGIGV DTLNTVMLTQ AGSSGTEGQ GQMLMQTIKL AFSITNNVIR LKPPSSGVSP LEHALTQHGA HGNNLIAVLA KYIYHRYDPS LPRLAIQLLK RLAMVAPMSV YACLGSDAA AIRDAFLSRL RDNIEDMQIK IMILEFLTVA VETQPGLIEL FLNLEAKDTN EGSKEYSLGE WSCLQVVLKL I DSQDPESS WGAPLLHRSA IAFLHALWQD RRDSAMTVLR TKPNFWENLT SPLFGTLACP SESSELSILE TCAFIMKIIC LE IYYAVRG SLGDSLKKIL KKFSEEERFT YWSNYVHSLV CQVAETEGTC NSLTEYQQLL SAWRMFLIVA THNADVMHLT NPE VRQKLF KDILGGTQAL LVVPRSVACM HLSSMLCTVM IILLRRWKND LAAPEDILNS LTQILEGVLQ RDQQLVEKTK AQIF SALIS VLEMKPMKAS EIPQYSQLLL NVCETLQEEV VSLVDHTRHE VPASDTSEDK DSMETEDTGR IRQKDQRDGV CVLGL HLAK ELCEADEEGD QWQQVLRKLP VLPILFSALE VSLRIKQNLH FCEAILHFLF TLAKTHQGAA AMAGAGITQT VCLPLL SVY QLSSNGAGSV QPAVSLRKSL DAPSWPGVYR LTVSLMERLL KTLRYNFLSE ALDFVGVHQE RILQCLSAVR TVQSLSC LE EADHTVGFLL QLSNFTKEWH FHLPQLIKDV QVNLCYLCQA CTSLLHSRKM LQHYLQIKNG ESMSSTATPR GQRTPQTP S KQPTAESEAL ELRQLRTVQH SLLKILGKTL ATLRAFTPDL CQILQVQPLD LAQYNLLFAL SFTTPAFDAD VTPSFGTLL ATVNVTLSML GEMDKKKDHP LSRALVESNN TGESKNNKSL LLFIMENCFY LLISQAVRYL RDPSVHPRDK QRMKQELSSE LSTLLSSLS RYFRRGGPSS PAGGLMPSPQ PKGASAAKVV PEAQEPLIQL VQAFVRHVQR

UniProtKB: Nucleoporin NUP188

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Macromolecule #3: Nuclear pore complex protein Nup93

MacromoleculeName: Nuclear pore complex protein Nup93 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 93.565156 KDa
SequenceString: MDGEGFGELL QQAEQLAAET EGVTELPHVE RNLQEIQQAG ERLRSKTMTR TSQESANVKA SVLLGSRGLD ISHISQRLES LSAATTFEP LEPVKDTDIQ GFLKNEKDNA LLSAIEESRK RTFVMAEEYH RESMLVEWEQ VKQRVLHTLL ASGEDALDFT Q ESETSYIS ...String:
MDGEGFGELL QQAEQLAAET EGVTELPHVE RNLQEIQQAG ERLRSKTMTR TSQESANVKA SVLLGSRGLD ISHISQRLES LSAATTFEP LEPVKDTDIQ GFLKNEKDNA LLSAIEESRK RTFVMAEEYH RESMLVEWEQ VKQRVLHTLL ASGEDALDFT Q ESETSYIS ESGAPGRSSL DNVEMAYARQ MYMYNEKVVS GHLQPSLVDL CTEAAERLDD KNVSDLWVMV KQMTDVPLIP AS DTLKSRC SGQMQMAFVR QALNYLEQSY KNYTLISVFA NLQQAQLGGV PGTYNLVRSF LNIRLPTPIP GLQDGEIEGY PVW ALIYYC MRCGDLMAAQ QVVNRAQHQL GDFKNCFQEY IHNKDRRLSP TTENKLRLHY RRAVRASTDP YKRAVYCIIG RCDV SDNHS EVADKTEDYL WLKLSQVCFE DEANSSPQDR LTLPQFQKQL FEDYGESHFA VNQQPYLYFQ VLFLTAQFEA AIAFL FRLE RTRCHAVHVA LALFELKLLL KSTGQSAQLL SQEPGEPQGV RRLNFIRLLM LYTRKFEPTD PREALQYFYF LRNEKD NQG ESMFLRCVSE LVIESREFDM LLGKLEKDGS RKPGAIDKFT RDTKTIINKV ASVAENKGLF EEAAKLYDLA KNPDKVL EL TNKLLSPVVS QISAPQSNRE RLKNMALAIA ERYKSQGVSA EKSINSTFYL LLDLITFFDE YHAGHIDLSF DVIERLKL V PLSQDSVEER VAAFRNFSDE IRHNLSEILL ATMNILFTQY KRLKGSGPTT LGRPQRVQED KDSVLRSQAR ALITFAGMI PYRMSGDTNA RLVQMEVLMN

UniProtKB: Nuclear pore complex protein Nup93

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Macromolecule #4: Nup155-prov protein

MacromoleculeName: Nup155-prov protein / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 154.922422 KDa
SequenceString: MPSATPGAPA ASAAMQEALE GAGRIIDRLL QEDRAYPDLS ELLNVPVHTC PTISGVSEMD YPLQSPGLLT IPSLPEISAI RRVPLPPEL IEQFGHMQCN CMMGVFPEIS RAWLTIDSDI FMWNYEDGGD LAYYDGLSET ILSVGLVKPK TGIFQPHIRF L LVLSTPVD ...String:
MPSATPGAPA ASAAMQEALE GAGRIIDRLL QEDRAYPDLS ELLNVPVHTC PTISGVSEMD YPLQSPGLLT IPSLPEISAI RRVPLPPEL IEQFGHMQCN CMMGVFPEIS RAWLTIDSDI FMWNYEDGGD LAYYDGLSET ILSVGLVKPK TGIFQPHIRF L LVLSTPVD IVILGLSFAN LQPGNLNDSI SGGMQLLPDP LYSLPTDNTY LLSITSTDNG RIFLSGKDGC LYEVEYQAEA GW FSQRCRK INHSKSSLSF LVPSVLQFAF SEDDPIVQIA IDNSRNILYT RSEKGVIQVY DLGVDGHGMS RVASVSQNSL VSA AGNIAR TIDRNVFKPI IHISVIEMSE SVNCHLLAVT HTGVRFYFST VPFKQPTARP CMLALVHVRL PPGFSASSNV EKPS KVHKA LYNNGVLLMA ASENEDNDML WCINRDSFPF QKPMMETQVT TQVDGHSWAL SAVDEQKADK IVTPLNKDLI PLTDS PVII QQHMIPPKRF VLLSAQGSHI FYKLRPVDQL RHLLVSNSGG DGEEIERFFK LHQENQACAT CLILACSSAA SDREVS SWA ARAFFRYGGE AQLRVQSALH APSNVGPIFG SPLPVASPIP VGSPMPNPSF LGTPTQGACP PNVSTPAYGV ATPAPQP PA VPGMMGTEIV FSGKHNGICI YFCRIIGNIW DGSVAVENTF QSGNREVTAI DSSVTPQHLE SVLKELKGLL EFLDRYSQ F TAGSLGNPGF GTPANRQQRL VSLGRPDIGS SQQAQQELQR KYHTEAQLAE QFSLQGIHQL VRKMCQALAL WKLLCEHQF SLVVSDLQKE LQEQLKITTF KDLVIRDKEL TGALTASLIS CYIRDNASVD GISYRLQEVC PLLYSTDDAV CSKANELLQR SRHVPNKQE KERMLRESLK EYQKISQQVD LPNVCAQYRQ VRFYEGVVEL CLSAAEKKDP QGLGLHFHKN GEPEEDMAGL Q AFQERLNS YKCITDTLQE LVNQSKAAPQ SPSVPKKPGP PVLSSDPNML SNEEAGIHFE QMLKLAQRSA DELFNIALFN WL IQADLTD KLLELNSPFL EPHLVRMAKL DQNKVRYMDL LWRYYEKNRN FSNAARVVAK LADMHSPEIS LKQRLEYISR AIL SAKSST TMSTLAADGE FLHELEEKLE VARIQLQIQE TLTRQYSHHS TVGDAVSQLD SQLMDITKMF GQYADPFRLS ECKL AIIHC AGHSDPILVQ TLWQDIIDKE LSDSMGNSSV DRMQSLHLKI TSLGKIYAST PRYFPLEFLV KYLEQQVCNF SWDAG FVTY TMQEINVPVP KLLEVYDHLF KARDPWWSRM KKPLHLLESI YILLSGYVQE PSKVPSYERR RFTTLCLDAI SCYLVE LQS MDPAPALLNT VSNFKSLQAK LERLS

UniProtKB: Nucleoporin 155kDa L homeolog

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Macromolecule #5: Nup54

MacromoleculeName: Nup54 / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 58.618617 KDa
SequenceString: MAFNFGATTG TPANQGTTGF SLGTFTPKTT TSGFGFGTTT TTAPTGFGGG FGGFGATTTA STGPAFSFTT PANTTSGLFG ATQNKGFGF GTGFGSTTTS TGLGTGLGTG LGFTGFNTSQ QQQQQSVLGA GLFNQSFQST PQSNQLINTA SALSAPTLLG D ERDAILAK ...String:
MAFNFGATTG TPANQGTTGF SLGTFTPKTT TSGFGFGTTT TTAPTGFGGG FGGFGATTTA STGPAFSFTT PANTTSGLFG ATQNKGFGF GTGFGSTTTS TGLGTGLGTG LGFTGFNTSQ QQQQQSVLGA GLFNQSFQST PQSNQLINTA SALSAPTLLG D ERDAILAK WNQLQAFWGT GKGFFMNNTP PVEFTQENPF CRFKAVGFSY IPNNKDEDGL ISLIFNKKES DIRGQQQQLV ES LHKVLGG HQTLTVNVEG VKTKADNQTE VIIYVVERSP NGTSRRVGAS ALFSYFEQAH IKANMQQLGV TGAMAQTELS PVQ IKQLIQ NPLSGVDPII WEQAKVDNPD PERLIPVPMI GFKELLRRLE VQDQMTKQHQ SRLDIISEDI GELQKNQTTT MAKI GQYKR KLMELSHRVL QVLIKQEIQR KSGFAIQAEE EQLRVQLDTI QSELNAPTQF KGRLNELMSQ IRMQNHFGAV RSEEK YYVD ADLLREIKQH LKQQQEGVSH LISIIKDNHE DIKLIEQGLN DNLHMRTGFL S

UniProtKB: Nucleoporin 54kDa S homeolog isoform X2

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Macromolecule #6: IL4I1 protein

MacromoleculeName: IL4I1 protein / type: protein_or_peptide / ID: 6 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 55.969496 KDa
SequenceString: MSGFNFGAAS AGGFSFGNPK STTTTAPTGF SFGAATAAPS GGFSFGTATP TPASTTGQTS GLFSFSNPAP SLAPTSGFSF GAQVTSTPA PSSGGLAFGA NTSKLNSGVG NQPAGGTTQT SQPMGGFSFG AATTQTQPSA TSVGGFSFAG GVGSTSTNVF A QPAASTGI ...String:
MSGFNFGAAS AGGFSFGNPK STTTTAPTGF SFGAATAAPS GGFSFGTATP TPASTTGQTS GLFSFSNPAP SLAPTSGFSF GAQVTSTPA PSSGGLAFGA NTSKLNSGVG NQPAGGTTQT SQPMGGFSFG AATTQTQPSA TSVGGFSFAG GVGSTSTNVF A QPAASTGI TLQSAVSTAA APTATTSQPT STFSFGTQPQ AAPALNFGLL SSSSVLSTAS TPAAAQPVAP TTGLSLNFGK PA DTSAAVT STGSTTTNTP SLSSLLGTSG PSLFSSVATS TVPSVVSTVA SGLSLTSTAT STGFGMKTLA SSAVPTGTLA TST ASLGVK APLAGTIVQA NAVGSAAATG ISTATAMTYA QLENLINKWS LELEDQEKHF LQQATQVNAW DRTLMQNGER ITTL HREME KVKLDQKRLD QELDFILSQQ KELEDLLTPL EESVKEQSGT IYLQHADEER EKTYKLAENI DAQLKRMAQD LKEVI EHLN TSAGPGDASN PLQQICKILN AHMDSLQWID QNSALLQRKV EQVTKECESR RKEQERGFSI AFD

UniProtKB: IL4I1 protein

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Macromolecule #7: MGC84997 protein

MacromoleculeName: MGC84997 protein / type: protein_or_peptide / ID: 7 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 61.216863 KDa
SequenceString: MASGFSFGTA AASTTTLNPT AAAPFSFGAT PAASNTGTTG GLGFGAFNAA ATPATTTATT GLGGGLFGAK PAAGFTLGGA NTATATTTA ASTGFSVGFN KPAGSATPFS LPVTSTSSGG LSLASALTST PATGPSPFTL NLGSTPATTT AAATGLSLGG T LTGLGGSL ...String:
MASGFSFGTA AASTTTLNPT AAAPFSFGAT PAASNTGTTG GLGFGAFNAA ATPATTTATT GLGGGLFGAK PAAGFTLGGA NTATATTTA ASTGFSVGFN KPAGSATPFS LPVTSTSSGG LSLASALTST PATGPSPFTL NLGSTPATTT AAATGLSLGG T LTGLGGSL FQNTNPSATG LGQSTLGQST LGQSTLGQSL LGQSLLGQSL LGQSTLGQST LGQSLLGQSL LGLGLNLGAV AP VSQVTTH EGLGGLDFSS SSDKKSDKAG TRPEDSKALK DENLPQLLCQ DVENFQKFVK EQKQVQEEIS RMSSKAMLKV QED IKALKQ LLSVASSGLQ RNALAIDKLK IETAEELKNA EIALRTQKTP PGLQHENTAP ADYFHTLVQQ FEVQLQQYRQ QIEE LENHL ATQSNTLHLS PQDLSMAMQK LYQTFVALAA QLQAVNENFK MLKEQYLGYR KAFLGDSTDV FEARRAEAKK WQNAP RVTT GPTPFSNIPN AAAVAMAATL TQQQQPTTGF GSSSAFGGNT SGSSSFGFGT ANKPSGSLSA GFGSTSTSGF NFSNPG INA SAGLTFGVSN PSSTSFGTGQ LLQLKKPPAG NKRGKR

UniProtKB: MGC84997 protein

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Macromolecule #8: Aaas-prov protein

MacromoleculeName: Aaas-prov protein / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 57.120965 KDa
SequenceString: MCSLDLFPPP LDGSQLPLYE FNNEIVAGKG FDNPPPTFQS ELVNIPEPTI PVDALKAPGR MELSSKTAFI HQKESIWKRC LNAWHNVGL AGFLEEMSNS KEEVPPWLCH VTRCSLAVCR SVSSLHGSLF PHLTISPQMK SEDLTAEFSQ ALGWADCPLR A FAWHPHTY ...String:
MCSLDLFPPP LDGSQLPLYE FNNEIVAGKG FDNPPPTFQS ELVNIPEPTI PVDALKAPGR MELSSKTAFI HQKESIWKRC LNAWHNVGL AGFLEEMSNS KEEVPPWLCH VTRCSLAVCR SVSSLHGSLF PHLTISPQMK SEDLTAEFSQ ALGWADCPLR A FAWHPHTY KFALALLDDS IRIYTAGSPT IPTLKHRLQK DVASLAWKPM CASVLAVACQ SCVLVWHVDP TSLSTRPSSG CA QVLSHPG HSPVTSVCWS PKGGVLLSAS PVDTAMLVWD VPTESCIPLQ RVGGGGVTFL SWSPDGSKVL AATPSSVFRV WET QKWTCE RWPTLQGRCQ TGCWSPDGSR LLFAVKGESV IYSLCFSVSE GEAQAGVGGS QSATVVADVS EVVFTTHTGE IRVG GEIQS MCWDPSGERL AVLLKGNPEF EESQPVIAVF RTRNSPIFEL LPCGFIHGRK GETPQLFQFH PGFNKGALLS QLWSS GRVN HFPFYFVNAQ CPRFSPESIA VVPGNTISTA NPRTLFTER

UniProtKB: Aaas-prov protein

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Macromolecule #9: Nucleoporin NDC1

MacromoleculeName: Nucleoporin NDC1 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 74.420305 KDa
SequenceString: MTMLGERLVL RWRVAASFAW SVILMPVCCA LFIVLSRIQI LHPIQWLTDS ISDLTSSYTI FCLLLICAIL GLQCTFLMEY YTVVPSIPC SRLALIGNLL LPHRILHSLA HVAMGVLASW CYAVLSKGKY QLLVVSCTLQ SEDEADKPSH CLNESHLFQL L CGAFFGYS ...String:
MTMLGERLVL RWRVAASFAW SVILMPVCCA LFIVLSRIQI LHPIQWLTDS ISDLTSSYTI FCLLLICAIL GLQCTFLMEY YTVVPSIPC SRLALIGNLL LPHRILHSLA HVAMGVLASW CYAVLSKGKY QLLVVSCTLQ SEDEADKPSH CLNESHLFQL L CGAFFGYS YSLQYFVHNM NYLSFPSIQQ YKYLQFRRFL PLIIKQSVFQ SLYFIRSYAI LYFCLGNIPR TWIQTALNLH MD RQQPSLD TLRGFLNLSL FYQIWLSGTF LLATWYMVWI LFRIYTTEAR IFPVQTSFAE EAEKCLPFIL NSNTLPLVKY LAM QDLVLL SQYSPSRRQE VFSLSQPGGH PHNWTSISKE CLNLMSSLTS RLIAHQEAAA NNGRMRVPSS PKQIRKSSSS SGTS LIEDS AEQTQNLSTI PRIGIPSLLK TASLKSSLDI GSPFATPGVK QMSESLDPNT PCHGSVQSPQ VTRRGAKLWT SDSDV QKNG SEVSPVMHRP VCNGAKQGIL HTWFQHKLVQ IKNVLSKRGL IMYLFSKHPE ASSQDVFADA QIHIWALEAL SHLVAA SFS EDRMGVVQTS LSSVLAILLT LQEAVEKHFK LPHASSKPAR NPGSLLDSSC KTLRFSLRAA LKTAIYRITT TFGEHLH AV PVSSEHKKKL QQFLDFKE

UniProtKB: Nucleoporin NDC1

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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 (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: 4.0 µm / Nominal defocus min: 1.2 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: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2093631
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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