EMDB-24258: Structure of the in situ yeast NPC

Basic information

• Entry: Database: EMDB / ID: EMD-24258
• Title: Structure of the in situ yeast NPC
• Map data: full in situ NPC map recombined from 90 degree wedge focused alignment

Sample

• Organelle or cellular component: yeast NPC
  • Protein or peptide: x 21 types

• Keywords: NPC / nucleocytoplasmic transport / TRANSLOCASE

Function / homology

Function:

response to spindle checkpoint signaling / nuclear pore linkers / peroxisomal importomer complex / regulation of protein desumoylation / mRNA export from nucleus in response to heat stress / nuclear pore inner ring / Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / protein localization to nuclear inner membrane / chromosome, subtelomeric region / COPII-mediated vesicle transport / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore localization / adenyl-nucleotide exchange factor activity / nuclear pore central transport channel / regulation of nucleocytoplasmic transport / establishment of mitotic spindle localization / nuclear migration along microtubule / regulation of TORC1 signaling / nuclear pore organization / nuclear pore outer ring / nuclear pore complex assembly / telomere tethering at nuclear periphery / COPII vesicle coat / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / positive regulation of protein exit from endoplasmic reticulum / 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 / cytoplasmic dynein complex / protein localization to kinetochore / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / SUMOylation of chromatin organization proteins / RNA export from nucleus / silent mating-type cassette heterochromatin formation / nucleocytoplasmic transport / vacuolar membrane / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / regulation of mitotic nuclear division / dynein intermediate chain binding / NLS-bearing protein import into nucleus / cytoplasmic microtubule / establishment of mitotic spindle orientation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / ribosomal large subunit export from nucleus / positive regulation of TOR signaling / subtelomeric heterochromatin formation / mRNA transport / mRNA export from nucleus / nuclear pore / ribosomal small subunit export from nucleus / ERAD pathway / Neutrophil degranulation / protein export from nucleus / positive regulation of TORC1 signaling / cellular response to amino acid starvation / nuclear periphery / cell periphery / chromosome segregation / promoter-specific chromatin binding / molecular condensate scaffold activity / heterochromatin formation / phospholipid binding / protein import into nucleus / transcription corepressor activity / double-strand break repair / protein transport / nuclear envelope / single-stranded DNA binding / cellular response to heat / nuclear membrane / amyloid fibril formation / chromosome, telomeric region / hydrolase activity / cell division / chromatin binding / endoplasmic reticulum membrane / protein-containing complex binding / positive regulation of DNA-templated transcription / structural molecule activity / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / identical protein binding / nucleus / cytosol / cytoplasm

Domain/homology:

Nucleoporin Nup159/Nup146, N-terminal / Nucleoporin or Nuclear pore complex subunit NUP214=Nup159 / Nucleoporin NUP120, helical domain / RNA-recognition motif (RRM) Nup35-type domain / Nucleoporin, NUP53 / Nucleoporin NUP88/NUP82 / 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 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 Nup85-like / Nucleoporin Nup120/160 / Nup85 Nucleoporin / Nuclear pore protein 84/107 / Nuclear pore protein 84 / 107 / Nuclear pore complex protein Nup133-like / 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 / Dynein light chain, type 1/2, conserved site / Dynein light chain type 1 signature. / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like / Sec13/Seh1 family / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Dynein light chain, type 1/2 / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin peptidase S59-like / Nucleoporin autopeptidase / NUP C-terminal domain profile. / Dynein light chain type 1 / Dynein light chain type 1 / Dynein light chain superfamily / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily

Component:

Nucleoporin NSP1 / Nucleoporin NIC96 / Nucleoporin NUP120 / Nucleoporin NUP133 / Nucleoporin NUP170 / Nucleoporin NUP157 / Nucleoporin NUP82 / Nucleoporin NUP159 / Nucleoporin NUP85 / Nucleoporin NUP192 / Nucleoporin NUP57 / Nucleoporin NUP145 / Nucleoporin NUP188 / Nucleoporin NUP84 / Nucleoporin SEH1 / Nucleoporin NUP49/NSP49 / Dynein light chain 1, cytoplasmic / Nucleoporin NUP53 / Protein transport protein SEC13 / Nucleoporin ASM4

• Biological species: Saccharomyces cerevisiae (brewer's yeast)
• Method: subtomogram averaging / cryo EM / Resolution: 37.0 Å
• Authors: Villa E / Singh D

Funding support

United States, 7 items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	DP2 GM123494	United States
National Science Foundation (NSF, United States)	MRI DBI 1920374	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	P01 GM121203	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R01 GM121443	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	P41 GM109824	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R01 GM121443	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R01 GM45377	United States

• Citation: Journal: 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 / 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-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

Deposition	Jun 17, 2021	-
Header (metadata) release	Jan 26, 2022	-
Map release	Jan 26, 2022	-
Update	Jun 5, 2024	-
Current status	Jun 5, 2024	Processing site: RCSB / Status: Released

Map

• File: Download / File: emd_24258.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: full in situ NPC map recombined from 90 degree wedge focused alignment
• Voxel size: X=Y=Z: 6.74 Å

Density

Contour Level	By AUTHOR: 1950.0 / Movie #1: 1950
Minimum - Maximum	-3.9280643 - 4082.771200000000135
Average (Standard dev.)	1772.169699999999921 (±428.825159999999983)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 320 320 320 Spacing 320 320 320
Cell	A=B=C: 2156.7998 Å α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	6.74	6.74	6.74
M x/y/z	320	320	320
origin x/y/z	0.000	0.000	0.000
length x/y/z	2156.800	2156.800	2156.800
α/β/γ	90.000	90.000	90.000
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	320	320	320
D min/max/mean	-3.928	4082.771	1772.170

Supplemental data

Mask #1

• File: emd_24258_msk_1.map

Mask #2

• File: emd_24258_msk_2.map

Mask #3

• File: emd_24258_msk_3.map

Additional map: zoned 3D map of Nsp1-FG-connections

• File: emd_24258_additional_1.map
• Annotation: zoned 3D map of Nsp1-FG-connections

Additional map: zoned 3D map of inner ring of spokes

• File: emd_24258_additional_2.map
• Annotation: zoned 3D map of inner ring of spokes

Additional map: full in situ NPC map recombined from 90...

• File: emd_24258_additional_3.map
• Annotation: full in situ NPC map recombined from 90 degree wedge focused alignment and masked to remove central channel density

Additional map: zoned 3D map of the N-ring

• File: emd_24258_additional_4.map
• Annotation: zoned 3D map of the N-ring

Additional map: zoned 3D map of C-ring plus Nup82 complex with 3 Dyn 2 dimers

• File: emd_24258_additional_5.map
• Annotation: zoned 3D map of C-ring plus Nup82 complex with 3 Dyn 2 dimers

Additional map: zoned 3D map of Pom152 ring

• File: emd_24258_additional_6.map
• Annotation: zoned 3D map of Pom152 ring

Additional map: difference map for pore membrane

• File: emd_24258_additional_7.map
• Annotation: difference map for pore membrane

Half map: half map

• File: emd_24258_half_map_1.map
• Annotation: half map

Half map: half map

• File: emd_24258_half_map_2.map
• Annotation: half map

Sample components

Entire : yeast NPC

• Entire: Name: yeast NPC

Components

• Organelle or cellular component: yeast NPC
  • Protein or peptide: Nucleoporin NUP170
  • Protein or peptide: Nucleoporin NUP157
  • Protein or peptide: orphans bound to Nup192 NTD
  • 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
  • Protein or peptide: Nucleoporin NUP82
  • Protein or peptide: Nucleoporin NUP159
  • Protein or peptide: Nucleoporin NUP120
  • Protein or peptide: Nucleoporin NUP85
  • Protein or peptide: Nucleoporin 145c
  • Protein or peptide: Protein transport protein SEC13
  • Protein or peptide: Nucleoporin SEH1
  • Protein or peptide: Nucleoporin NUP84
  • Protein or peptide: Nucleoporin NUP133
  • Protein or peptide: Dynein light chain 1, cytoplasmic

Supramolecule #1: yeast NPC

• Supramolecule: Name: yeast NPC / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Complete yeast NPC from vitrified cells
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast)
• Molecular weight: Theoretical: 52.0 MDa

Macromolecule #1: Nucleoporin NUP170

• Macromolecule: Name: Nucleoporin NUP170 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast)
• Molecular weight: Theoretical: 169.651969 KDa

Sequence

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

Macromolecule #2: Nucleoporin NUP157

• Macromolecule: Name: Nucleoporin NUP157 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast)
• Molecular weight: Theoretical: 156.827484 KDa

Sequence

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

Macromolecule #3: orphans bound to Nup192 NTD

• Macromolecule: Name: orphans bound to Nup192 NTD / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast)
• Molecular weight: Theoretical: 3.08179 KDa

Sequence

String:

(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)

Macromolecule #4: Nucleoporin NSP1

• Macromolecule: Name: Nucleoporin NSP1 / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast)
• Molecular weight: Theoretical: 86.611672 KDa

Sequence

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

Macromolecule #5: Nucleoporin NUP57

• Macromolecule: Name: Nucleoporin NUP57 / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast)
• Molecular weight: Theoretical: 57.547145 KDa

Sequence

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

Macromolecule #6: Nucleoporin NUP49/NSP49

• Macromolecule: Name: Nucleoporin NUP49/NSP49 / type: protein_or_peptide / ID: 6 / Number of copies: 4 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast)
• Molecular weight: Theoretical: 49.174762 KDa

Sequence

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

Macromolecule #7: Nucleoporin NUP192

• Macromolecule: Name: Nucleoporin NUP192 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast)
• Molecular weight: Theoretical: 191.718125 KDa

Sequence

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

Macromolecule #8: Nucleoporin NUP188

• Macromolecule: Name: Nucleoporin NUP188 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast)
• Molecular weight: Theoretical: 188.753281 KDa

Sequence

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

Macromolecule #9: Nucleoporin NIC96

• Macromolecule: Name: Nucleoporin NIC96 / type: protein_or_peptide / ID: 9 / Number of copies: 4 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast)
• Molecular weight: Theoretical: 96.291586 KDa

Sequence

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

Macromolecule #10: Nucleoporin NUP53

• Macromolecule: Name: Nucleoporin NUP53 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast)
• Molecular weight: Theoretical: 52.688668 KDa

Sequence

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

UniProtKB: Nucleoporin NUP53

Macromolecule #11: Nucleoporin ASM4

• Macromolecule: Name: Nucleoporin ASM4 / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast)
• Molecular weight: Theoretical: 58.853902 KDa

Sequence

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

UniProtKB: Nucleoporin ASM4

Macromolecule #12: Nucleoporin NUP82

• Macromolecule: Name: Nucleoporin NUP82 / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast)
• Molecular weight: Theoretical: 82.174047 KDa

Sequence

String:

MSQSSRLSAL PIFQASLSAS QSPRYIFSSQ NGTRIVFIQD NIIRWYNVLT DSLYHSLNFS RHLVLDDTFH VISSTSGDLL CLFNDNEIF VMEVPWGYSN VEDVSIQDAF QIFHYSIDEE EVGPKSSIKK VLFHPKSYRD SCIVVLKEDD TITMFDILNS Q EKPIVLNK PNNSFGLDAR VNDITDLEFS KDGLTLYCLN TTEGGDIFAF YPFLPSVLLL NEKDLNLILN KSLVMYESLD ST TDVIVKR NVIKQLQFVS KLHENWNSRF GKVDIQKEYR LAKVQGPFTI NPFPGELYDY TATNIATILI DNGQNEIVCV SFD DGSLIL LFKDLEMSMS WDVDNYVYNN SLVLIERVKL QREIKSLITL PEQLGKLYVI SDNIIQQVNF MSWASTLSKC INES DLNPL AGLKFESKLE DIATIERIPN LAYINWNDQS NLALMSNKTL TFQNISSDMK PQSTAAETSI STEKSDTVGD GFKMS FTQP INEILILNDN FQKACISPCE RIIPSADRQI PLKNEASENQ LEIFTDISKE FLQRIVKAQT LGVSIHNRIH EQQFEL TRQ LQSTCKIISK DDDLRRKFEA QNKKWDAQLS RQSELMERFS KLSKKLSQIA ESNKFKEKKI SHGEMKWFKE IRNQILQ FN SFVHSQKSLQ QDLSYLKSEL TRIEAETIKV DKKSQNEWDE LRKMLEIDSK IIKECNEELL QVSQEFTTKT Q

UniProtKB: Nucleoporin NUP82

Macromolecule #13: Nucleoporin NUP159

• Macromolecule: Name: Nucleoporin NUP159 / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast)
• Molecular weight: Theoretical: 159.067188 KDa

Sequence

String:

MSSLKDEVPT ETSEDFGFKF LGQKQILPSF NEKLPFASLQ NLDISNSKSL FVAASGSKAV VGELQLLRDH ITSDSTPLTF KWEKEIPDV IFVCFHGDQV LVSTRNALYS LDLEELSEFR TVTSFEKPVF QLKNVNNTLV ILNSVNDLSA LDLRTKSTKQ L AQNVTSFD VTNSQLAVLL KDRSFQSFAW RNGEMEKQFE FSLPSELEEL PVEEYSPLSV TILSPQDFLA VFGNVISETD DE VSYDQKM YIIKHIDGSA SFQETFDITP PFGQIVRFPY MYKVTLSGLI EPDANVNVLA SSCSSEVSIW DSKQVIEPSQ DSE RAVLPI SEETDKDTNP IGVAVDVVTS GTILEPCSGV DTIERLPLVY ILNNEGSLQI VGLFHVAAIK SGHYSINLES LEHE KSLSP TSEKIPIAGQ EQEEKKKNNE SSKALSENPF TSANTSGFTF LKTQPAAANS LQSQSSSTFG APSFGSSAFK IDLPS VSST STGVASSEQD ATDPASAKPV FGKPAFGAIA KEPSTSEYAF GKPSFGAPSF GSGKSSVESP ASGSAFGKPS FGTPSF GSG NSSVEPPASG SAFGKPSFGT PSFGSGNSSA EPPASGSAFG KPSFGTSAFG TASSNETNSG SIFGKAAFGS SSFAPAN NE LFGSNFTISK PTVDSPKEVD STSPFPSSGD QSEDESKSDV DSSSTPFGTK PNTSTKPKTN AFDFGSSSFG SGFSKALE S VGSDTTFKFG TQASPFSSQL GNKSPFSSFT KDDTENGSLS KGSTSEINDD NEEHESNGPN VSGNDLTDST VEQTSSTRL PETPSDEDGE VVEEEAQKSP IGKLTETIKK SANIDMAGLK NPVFGNHVKA KSESPFSAFA TNITKPSSTT PAFSFGNSTM NKSNTSTVS PMEEADTKET SEKGPITLKS VENPFLPAKE ERTGESSKKD HNDDPKDGYV SGSEISVRTS ESAFDTTANE E IPKSQDVN NHEKSETDPK YSQHAVVDHD NKSKEMNETS KNNERSGQPN HGVQGDGIAL KKDNEKENFD SNMAIKQFED HQ SSEEDAS EKDSRQSSEV KESDDNMSLN SDRDESISES YDKLEDINTD ELPHGGEAFK AREVSASADF DVQTSLEDNY AES GIQTDL SESSKENEVQ TDAIPVKHNS TQTVKKEAVD NGLQTEPVET CNFSVQTFEG DENYLAEQCK PKQLKEYYTS AKVS NIPFV SQNSTLRLIE STFQTVEAEF TVLMENIRNM DTFFTDQSSI PLVKRTVRSI NNLYTWRIPE AEILLNIQNN IKCEQ MQIT NANIQDLKEK VTDYVRKDIA QITEDVANAK EEYLFLMHFD DASSGYVKDL STHQFRMQKT LRQKLFDVSA KINHTE ELL NILKLFTVKN KRLDDNPLVA KLAKESLARD GLLKEIKLLR EQVSRLQLEE KGKKASSFDA SSSITKDMKG FKVVEVG LA MNTKKQIGDF FKNLNMAK

UniProtKB: Nucleoporin NUP159

Macromolecule #14: Nucleoporin NUP120

• Macromolecule: Name: Nucleoporin NUP120 / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast)
• Molecular weight: Theoretical: 120.560328 KDa

Sequence

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

Macromolecule #15: Nucleoporin NUP85

• Macromolecule: Name: Nucleoporin NUP85 / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast)
• Molecular weight: Theoretical: 84.972438 KDa

Sequence

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

Macromolecule #16: Nucleoporin 145c

• Macromolecule: Name: Nucleoporin 145c / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast)
• Molecular weight: Theoretical: 81.157852 KDa

Sequence

String:

SIWGLVNEED AEIDEDDLSK QEDGGEQPLR KVRTLAQSKP SDKEVILKTD GTFGTLSGKD DSIVEEKAYE PDLSDADFEG IEASPKLDV SKDWVEQLIL AGSSLRSVFA TSKEFDGPCQ NEIDLLFSEC NDEIDNAKLI MKERRFTASY TFAKFSTGSM L LTKDIVGK SGVSIKRLPT ELQRKFLFDD VYLDKEIEKV TIEARKSNPY PQISESSLLF KDALDYMEKT SSDYNLWKLS SI LFDPVSY PYKTDNDQVK MALLKKERHC RLTSWIVSQI GPEIEEKIRN SSNEIEQIFL YLLLNDVVRA SKLAIESKNG HLS VLISYL GSNDPRIRDL AELQLQKWST GGCSIDKNIS KIYKLLSGSP FEGLFSLKEL ESEFSWLCLL NLTLCYGQID EYSL ESLVQ SHLDKFSLPY DDPIGVIFQL YAANENTEKL YKEVRQRTNA LDVQFCWYLI QTLRFNGTRV FSKETSDEAT FAFAA QLEF AQLHGHSLFV SCFLNDDKAA EDTIKRLVMR EITLLRASTN DHILNRLKIP SQLIFNAQAL KDRYEGNYLS EVQNLL LGS SYDLAEMAIV TSLGPRLLLS NNPVQNNELK TLREILNEFP DSERDKWSVS INVFEVYLKL VLDNVETQET IDSLISG MK IFYDQYKHCR EVAACCNVMS QEIVSKILEK NNPSIGDSKA KLLELPLGQP EKAYLRGEFA QDLMKCTYKI

UniProtKB: Nucleoporin NUP145

Macromolecule #17: Protein transport protein SEC13

• Macromolecule: Name: Protein transport protein SEC13 / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast)
• Molecular weight: Theoretical: 33.082965 KDa

Sequence

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

Macromolecule #18: Nucleoporin SEH1

• Macromolecule: Name: Nucleoporin SEH1 / type: protein_or_peptide / ID: 18 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast)
• Molecular weight: Theoretical: 39.170758 KDa

Sequence

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 KLSPLASEES LTNSNMFDNS ADVDMDAQGR SDSNTEEKAE LQSNLQVELL SEHDDHNGEV WSVSWNLTGT ILS SAGDDG KVRLWKATYS NEFKCMSVIT AQQ

UniProtKB: Nucleoporin SEH1

Macromolecule #19: Nucleoporin NUP84

• Macromolecule: Name: Nucleoporin NUP84 / type: protein_or_peptide / ID: 19 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast)
• Molecular weight: Theoretical: 83.718867 KDa

Sequence

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

Macromolecule #20: Nucleoporin NUP133

• Macromolecule: Name: Nucleoporin NUP133 / type: protein_or_peptide / ID: 20 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast)
• Molecular weight: Theoretical: 133.452672 KDa

Sequence

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: Nucleoporin NUP133

Macromolecule #21: Dynein light chain 1, cytoplasmic

• Macromolecule: Name: Dynein light chain 1, cytoplasmic / type: protein_or_peptide / ID: 21 / Number of copies: 6 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast)
• Molecular weight: Theoretical: 10.45698 KDa

Sequence

String:

MSDENKSTPI VKASDITDKL KEDILTISKD ALDKYQLERD IAGTVKKQLD VKYGNTWHVI VGKNFGSYVT HEKGHFVYFY IGPLAFLVF KTA

UniProtKB: Dynein light chain 1, cytoplasmic

Experimental details

Structure determination

• Method: cryo EM
• Processing: subtomogram averaging
• Aggregation state: cell

Sample preparation

• Buffer: pH: 7.5
• Grid: Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Pressure: 0.039 kPa
• Vitrification: Cryogen name: ETHANE-PROPANE; Details: A custom-built vitrification device (Max Planck Institute for Biochemistry, Munich).
• Details: W303 yeast cells were harvested during log-phase growth and diluted to an 0.8 x 107 cells/mL in YPD media. Five uL of this diluted sample was applied to glow-discharged 200-mesh, Quantafoil R2/1 grids (Electron Microscopy Sciences), excess media was manually blotted from the grid back side (opposite to the carbon substrate where the cells were deposited) and the grid was plunge frozen in a liquid ethane-propane mixture (50/50 volume, Airgas) then cryogenic, FIB milling was performed in an Aquilos DualBeam (Thermo Fisher Scientific)

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Specialist optics: Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
• Details: Tilt series collection: dose-symmetric & bi-directional
• Image recording: Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3708 pixel / Average exposure time: 2.0 sec. / Average electron dose: 4.5 e/Ų; Details: Images were collected in movie-mode at ~8 frames per second
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Calibrated defocus max: 6.0 µm / Calibrated defocus min: 2.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 42000
• Sample stage: Cooling holder cryogen: NITROGEN
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Details: The tilt images were motion-corrected but not dose-weighted.
• Final reconstruction: Number classes used: 1 / Applied symmetry - Point group: C₈ (8 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 37.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 (ver. 2.9) / Number subtomograms used: 518
• Extraction: Number tomograms: 293 / Number images used: 577 / Method: Manual boxing; Details: The full nuclear pores were manually identified in the tomograms for the manual boxing.
• Final angle assignment: Type: NOT APPLICABLE

Atomic model buiding 1

• Details: Manual docking and limited molecular dynamics flexible fitting
• Refinement: Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: cross-correlation

Output model

PDB-7n9f:
Structure of the in situ yeast NPC