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- EMDB-24232: Inner ring spoke from the isolated yeast NPC -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-24232
TitleInner ring spoke from the isolated yeast NPC
Map datarecombined full inner ring of spokes
Sample
  • Complex: spoke from yeast inner ring
    • Protein or peptide: x 11 types
Function / homology
Function and homology information


response to spindle checkpoint signaling / nuclear pore linkers / : / regulation of protein desumoylation / mRNA export from nucleus in response to heat stress / nuclear pore inner ring / protein localization to nuclear inner membrane / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore central transport channel / telomere tethering at nuclear periphery ...response to spindle checkpoint signaling / nuclear pore linkers / : / regulation of protein desumoylation / mRNA export from nucleus in response to heat stress / nuclear pore inner ring / protein localization to nuclear inner membrane / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore central transport channel / telomere tethering at nuclear periphery / regulation of nucleocytoplasmic transport / nuclear pore organization / nuclear pore complex assembly / tRNA export from nucleus / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / nuclear pore nuclear basket / RNA export from nucleus / protein localization to kinetochore / structural constituent of nuclear pore / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / regulation of mitotic nuclear division / NLS-bearing protein import into nucleus / ribosomal small subunit export from nucleus / ribosomal large subunit export from nucleus / mRNA transport / heterochromatin formation / nuclear pore / nuclear periphery / chromosome segregation / promoter-specific chromatin binding / phospholipid binding / protein import into nucleus / protein transport / single-stranded DNA binding / nuclear envelope / nuclear membrane / molecular adaptor activity / cell cycle / cell division / chromatin binding / protein-containing complex binding / positive regulation of DNA-templated transcription / DNA binding / RNA binding / identical protein binding / nucleus
Similarity search - Function
RNA-recognition motif (RRM) Nup35-type domain / Nucleoporin, NUP53 / Nup53/35/40-type RNA recognition motif / RNA-recognition motif (RRM) Nup35-type domain profile. / Nuclear pore protein Nup188, C-terminal / Nuclear pore protein NUP188 C-terminal domain / Nucleoporin Nup188, N-terminal / Nucleoporin p58/p45 / Nucleoporin Nup188, N-terminal / : ...RNA-recognition motif (RRM) Nup35-type domain / Nucleoporin, NUP53 / Nup53/35/40-type RNA recognition motif / RNA-recognition motif (RRM) Nup35-type domain profile. / Nuclear pore protein Nup188, C-terminal / Nuclear pore protein NUP188 C-terminal domain / Nucleoporin Nup188, N-terminal / Nucleoporin p58/p45 / Nucleoporin Nup188, N-terminal / : / Nucleoporin Nup188, N-terminal subdomain III / Nucleoporin, NSP1-like, C-terminal / Nucleoporin Nup54/Nup57/Nup44 / Nucleoporin Nup54, alpha-helical domain / Nucleoporin NSP1/NUP62 / Nucleoporin Nup188 / Nsp1-like C-terminal region / Nucleoporin complex subunit 54 / 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 interacting component Nup93/Nic96 / Nup93/Nic96 / Nucleoporin FG repeat / Nucleoporin FG repeat region / Nucleoporin, Nup133/Nup155-like, C-terminal / Non-repetitive/WGA-negative nucleoporin C-terminal / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Nucleoporin NSP1 / Nucleoporin NIC96 / Nucleoporin NUP170 / Nucleoporin NUP157 / Nucleoporin NUP192 / Nucleoporin NUP57 / Nucleoporin NUP188 / Nucleoporin NUP49/NSP49 / Nucleoporin NUP53 / Nucleoporin ASM4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Baker's yeast (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.6 Å
AuthorsAkey CW / Rout MP / Ouch C / Echevarria I / Fernandez-Martinez J / Nudelman I
Funding support United States, 3 items
OrganizationGrant numberCountry
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
CitationJournal: Cell / Year: 2022
Title: Comprehensive structure and functional adaptations of the yeast nuclear pore complex.
Authors: Christopher W Akey / Digvijay Singh / Christna Ouch / Ignacia Echeverria / Ilona Nudelman / Joseph M Varberg / Zulin Yu / Fei Fang / Yi Shi / Junjie Wang / Daniel Salzberg / Kangkang Song / ...Authors: Christopher W Akey / Digvijay Singh / Christna Ouch / Ignacia Echeverria / Ilona Nudelman / Joseph M Varberg / Zulin Yu / Fei Fang / Yi Shi / Junjie Wang / Daniel Salzberg / Kangkang Song / Chen Xu / James C Gumbart / Sergey Suslov / Jay Unruh / Sue L Jaspersen / Brian T Chait / Andrej Sali / Javier Fernandez-Martinez / Steven J Ludtke / Elizabeth Villa / Michael P Rout /
Abstract: Nuclear pore complexes (NPCs) mediate the nucleocytoplasmic transport of macromolecules. Here we provide a structure of the isolated yeast NPC in which the inner ring is resolved by cryo-EM at sub- ...Nuclear pore complexes (NPCs) mediate the nucleocytoplasmic transport of macromolecules. Here we provide a structure of the isolated yeast NPC in which the inner ring is resolved by cryo-EM at sub-nanometer resolution to show how flexible connectors tie together different structural and functional layers. These connectors may be targets for phosphorylation and regulated disassembly in cells with an open mitosis. Moreover, some nucleoporin pairs and transport factors have similar interaction motifs, which suggests an evolutionary and mechanistic link between assembly and transport. We provide evidence for three major NPC variants that may foreshadow functional specializations at the nuclear periphery. Cryo-electron tomography extended these studies, providing a model of the in situ NPC with a radially expanded inner ring. Our comprehensive model reveals features of the nuclear basket and central transporter, suggests a role for the lumenal Pom152 ring in restricting dilation, and highlights structural plasticity that may be required for transport.
History
DepositionJun 13, 2021-
Header (metadata) releaseJan 26, 2022-
Map releaseJan 26, 2022-
UpdateFeb 2, 2022-
Current statusFeb 2, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.595
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.595
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7n85
  • Surface level: 0.595
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7n85
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24232.png

Downloads & links

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Map

FileDownload / File: emd_24232.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationrecombined full inner ring of spokes
Voxel sizeX=Y=Z: 2.66 Å
Density
Contour LevelBy AUTHOR: 0.595 / Movie #1: 0.595
Minimum - Maximum0.0 - 4.327462
Average (Standard dev.)0.018599069 (±0.121410735)
SymmetrySpace group: 1
Details

EMDB XML:

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

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.662.662.66
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z1276.8001276.8001276.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean0.0004.3270.019

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Supplemental data

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Mask #1

Fileemd_24232_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: zoned single spoke

Fileemd_24232_additional_1.map
Annotationzoned single spoke
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: post-process focused spoke refinement after multibody

Fileemd_24232_additional_2.map
Annotationpost-process focused spoke refinement after multibody
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map focused spoke refinement

Fileemd_24232_half_map_1.map
Annotationhalf map focused spoke refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map focused spoke refinement

Fileemd_24232_half_map_2.map
Annotationhalf map focused spoke refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : spoke from yeast inner ring

EntireName: spoke from yeast inner ring
Components
  • Complex: spoke from yeast inner ring
    • Protein or peptide: Nucleoporin NUP170
    • Protein or peptide: Nucleoporin NUP157
    • Protein or peptide: Unknown connectors
    • Protein or peptide: Nucleoporin NSP1
    • Protein or peptide: Nucleoporin NUP57
    • Protein or peptide: Nucleoporin NUP49/NSP49
    • Protein or peptide: Nucleoporin NUP192
    • Protein or peptide: Nucleoporin NUP188
    • Protein or peptide: Nucleoporin NIC96
    • Protein or peptide: Nucleoporin NUP53
    • Protein or peptide: Nucleoporin ASM4

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Supramolecule #1: spoke from yeast inner ring

SupramoleculeName: spoke from yeast inner ring / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: recombined inner ring from spoke multi-body and focused 3D refinements with isolated NPC
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Location in cell: nuclear envelope
Molecular weightExperimental: 16.0 MDa

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Macromolecule #1: Nucleoporin NUP170

MacromoleculeName: Nucleoporin NUP170 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast)
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

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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: Baker's yeast (brewer's yeast)
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

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Macromolecule #3: Unknown connectors

MacromoleculeName: Unknown connectors / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 3.08179 KDa
SequenceString:
(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)

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Macromolecule #4: Nucleoporin NSP1

MacromoleculeName: Nucleoporin NSP1 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast)
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

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Macromolecule #5: Nucleoporin NUP57

MacromoleculeName: Nucleoporin NUP57 / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast)
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

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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: Baker's yeast (brewer's yeast)
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

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Macromolecule #7: Nucleoporin NUP192

MacromoleculeName: Nucleoporin NUP192 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast)
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

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Macromolecule #8: Nucleoporin NUP188

MacromoleculeName: Nucleoporin NUP188 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast)
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

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Macromolecule #9: Nucleoporin NIC96

MacromoleculeName: Nucleoporin NIC96 / type: protein_or_peptide / ID: 9 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast)
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

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Macromolecule #10: Nucleoporin NUP53

MacromoleculeName: Nucleoporin NUP53 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast)
Molecular weightTheoretical: 52.688668 KDa
SequenceString: MADLQKQENS SRFTNVSVIA PESQGQHEQQ KQQEQLEQQK QPTGLLKGLN GFPSAPQPLF MEDPPSTVSG ELNDNPAWFN NPRKRAIPN SIIKRSNGQS LSPVRSDSAD VPAFSNSNGF NNVTFGSKKD PRILKNVSPN DNNSANNNAH SSDLGTVVFD S NEAPPKTS ...String:
MADLQKQENS SRFTNVSVIA PESQGQHEQQ KQQEQLEQQK QPTGLLKGLN GFPSAPQPLF MEDPPSTVSG ELNDNPAWFN NPRKRAIPN SIIKRSNGQS LSPVRSDSAD VPAFSNSNGF NNVTFGSKKD PRILKNVSPN DNNSANNNAH SSDLGTVVFD S NEAPPKTS LADWQKEDGI FSSKTDNIED PNLSSNITFD GKPTATPSPF RPLEKTSRIL NFFDKNTKTT PNTASSEASA GS KEGASTN WDDHAIIIFG YPETIANSII LHFANFGEIL EDFRVIKDFK KLNSKNMSKS PSLTAQKYPI YTGDGWVKLT YKS ELSKSR ALQENGIIMN GTLIGCVSYS PAALKQLASL KKSEEIINNK TSSQTSLSSK DLSNYRKTEG IFEKAKAKAV TSKV RNAEF KVSKNSTSFK NPRRLEIKDG RSLFLRNRGK IHSGVLSSIE SDLKKREQAS KSKKSWLNRL NNWLFGWNDL

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Macromolecule #11: Nucleoporin ASM4

MacromoleculeName: Nucleoporin ASM4 / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast)
Molecular weightTheoretical: 58.853902 KDa
SequenceString: MFGIRSGNNN GGFTNLTSQA PQTTQMFQSQ SQLQPQPQPQ PQQQQQHLQF NGSSDASSLR FGNSLSNTVN ANNYSSNIGN NSINNNNIK NGTNNISQHG QGNNPSWVNN PKKRFTPHTV IRRKTTKQNS SSDINQNDDS SSMNATMRNF SKQNQDSKHN E RNKSAANN ...String:
MFGIRSGNNN GGFTNLTSQA PQTTQMFQSQ SQLQPQPQPQ PQQQQQHLQF NGSSDASSLR FGNSLSNTVN ANNYSSNIGN NSINNNNIK NGTNNISQHG QGNNPSWVNN PKKRFTPHTV IRRKTTKQNS SSDINQNDDS SSMNATMRNF SKQNQDSKHN E RNKSAANN DINSLLSNFN DIPPSVTLQD WQREDEFGSI PSLTTQFVTD KYTAKKTNRS AYDSKNTPNV FDKDSYVRIA NI EQNHLDN NYNTAETNNK VHETSSKSSS LSAIIVFGYP ESISNELIEH FSHFGHIMED FQVLRLGRGI NPNTFRIFHN HDT GCDEND STVNKSITLK GRNNESNNKK YPIFTGESWV KLTYNSPSSA LRALQENGTI FRGSLIGCIP YSKNAVEQLA GCKI DNVDD IGEFNVSMYQ NSSTSSTSNT PSPPNVIITD GTLLREDDNT PAGHAGNPTN ISSPIVANSP NKRLDVIDGK LPFMQ NAGP NSNIPNLLRN LESKMRQQEA KYRNNEPAGF THKLSNWLFG WNDL

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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

Concentration0.3 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMHEPES
50.0 mMpotassium acetate
20.0 mMsodium chlorideNaClSodium chloride
2.0 mMmagnesium chloride
1.0 mMDTT
0.1 percent wt/wtDeoxyBigChaps
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 5.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK III
Detailsinner ring spoke imaged from isolated yeast NPC

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.8000000000000003 µm / Calibrated defocus min: 1.5 µm / Calibrated magnification: 37651 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 50000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageCooling holder cryogen: NITROGEN
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 - Sampling interval: 5.0 µm / Digitization - Frames/image: 2-40 / Number grids imaged: 1 / Number real images: 4015 / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.18)
Startup modelType of model: EMDB MAP
EMDB ID:

7321

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 7.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0)
Details: 1.5x spoke from multibody and focused refinements after re-extraction of particles
Number images used: 145000
FSC plot (resolution estimation)

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Atomic model buiding 1

Detailsinitial spoke model from PDBDEV_00000012, rigid body dock with chimera and fitting with MDFF
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7n85:
Inner ring spoke from the isolated yeast NPC

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