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- EMDB-31891: Structure of Xenopus laevis NPC nuclear ring asymmetric unit -

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Basic information

Entry
Database: EMDB / ID: EMD-31891
TitleStructure of Xenopus laevis NPC nuclear ring asymmetric unit
Map data
Sample
  • Complex: nuclear pore complexNuclear pore
    • Protein or peptide: x 12 types
Function / homology
Function and homology information


GATOR2 complex / nephron development / nuclear pore organization / nuclear pore outer ring / nuclear pore complex assembly / attachment of mitotic spindle microtubules to kinetochore / structural constituent of nuclear pore / mitotic metaphase chromosome alignment / cellular response to nutrient levels / mRNA transport ...GATOR2 complex / nephron development / nuclear pore organization / nuclear pore outer ring / nuclear pore complex assembly / attachment of mitotic spindle microtubules to kinetochore / structural constituent of nuclear pore / mitotic metaphase chromosome alignment / cellular response to nutrient levels / mRNA transport / nuclear pore / positive regulation of TORC1 signaling / nuclear periphery / kinetochore / protein transport / nuclear membrane / lysosomal membrane / cell division / structural molecule activity / DNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
ELYS-like domain / ELYS, beta-propeller domain / Nuclear pore complex assembly / beta-propeller of ELYS nucleoporin / Nuclear pore complex protein NUP98-NUP96 / Nucleoporin Nup37 / Nucleoporin Nup85-like / Nup85 Nucleoporin / Nuclear pore protein 84/107 / Nuclear pore protein 84 / 107 ...ELYS-like domain / ELYS, beta-propeller domain / Nuclear pore complex assembly / beta-propeller of ELYS nucleoporin / Nuclear pore complex protein NUP98-NUP96 / Nucleoporin Nup37 / Nucleoporin Nup85-like / Nup85 Nucleoporin / Nuclear pore protein 84/107 / Nuclear pore protein 84 / 107 / Nuclear pore complex protein Nup133-like / Nucleoporin Nup186/Nup192/Nup205 / Nuclear pore complex scaffold, nucleoporins 186/192/205 / Nucleoporin interacting component Nup93/Nic96 / Nup93/Nic96 / Nucleoporin, Nup133/Nup155-like, C-terminal / Nucleoporin FG repeat / Nucleoporin FG repeat region / Non-repetitive/WGA-negative nucleoporin C-terminal / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like / Sec13/Seh1 family / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin autopeptidase / NUP C-terminal domain profile. / Nucleoporin peptidase S59-like / Quinoprotein alcohol dehydrogenase-like superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Nuclear pore complex protein Nup98-Nup96 / Nuclear pore complex protein Nup133 / Nuclear pore complex protein / MGC154553 protein / Nucleoporin SEH1-A / Protein ELYS / MGC83295 protein / MGC83926 protein / Nuclear pore complex protein Nup85 / Nuclear pore complex protein Nup93 / Protein SEC13 homolog
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog) / African clawed frog (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.1 Å
AuthorsTai L / Zhu Y / Sun F
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Protein Cell / Year: 2022
Title: 8 Å structure of the outer rings of the Xenopus laevis nuclear pore complex obtained by cryo-EM and AI.
Authors: Linhua Tai / Yun Zhu / He Ren / Xiaojun Huang / Chuanmao Zhang / Fei Sun /
Abstract: The nuclear pore complex (NPC), one of the largest protein complexes in eukaryotes, serves as a physical gate to regulate nucleocytoplasmic transport. Here, we determined the 8 Å resolution cryo- ...The nuclear pore complex (NPC), one of the largest protein complexes in eukaryotes, serves as a physical gate to regulate nucleocytoplasmic transport. Here, we determined the 8 Å resolution cryo-electron microscopic (cryo-EM) structure of the outer rings containing nuclear ring (NR) and cytoplasmic ring (CR) from the Xenopus laevis NPC, with local resolutions reaching 4.9 Å. With the aid of AlphaFold2, we managed to build a pseudoatomic model of the outer rings, including the Y complexes and flanking components. In this most comprehensive and accurate model of outer rings to date, the almost complete Y complex structure exhibits much tighter interaction in the hub region. In addition to two copies of Y complexes, each asymmetric subunit in CR contains five copies of Nup358, two copies of the Nup214 complex, two copies of Nup205 and one copy of newly identified Nup93, while that in NR contains one copy of Nup205, one copy of ELYS and one copy of Nup93. These in-depth structural features represent a great advance in understanding the assembly of NPCs.
History
DepositionSep 3, 2021-
Header (metadata) releaseFeb 2, 2022-
Map releaseFeb 2, 2022-
UpdateJul 13, 2022-
Current statusJul 13, 2022Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7vci
  • Surface level: 0.4
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7vci
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31891.png

Downloads & links

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Map

FileDownload / File: emd_31891.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 2.24 Å
Density
Contour LevelBy AUTHOR: 0.4 / Movie #1: 0.4
Minimum - Maximum-2.1325743 - 3.300856
Average (Standard dev.)0.008229044 (±0.091990344)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 716.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.242.242.24
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z716.800716.800716.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-2.1333.3010.008

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Supplemental data

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Mask #1

Fileemd_31891_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_31891_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_31891_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : nuclear pore complex

EntireName: nuclear pore complexNuclear pore
Components
  • Complex: nuclear pore complexNuclear pore
    • Protein or peptide: Nuclear pore complex protein Nup85Nuclear pore
    • Protein or peptide: MGC154553 protein
    • Protein or peptide: Nucleoporin SEH1-A
    • Protein or peptide: Nup160Nucleoporin 160
    • Protein or peptide: MGC83926 protein
    • Protein or peptide: Nuclear pore complex protein Nup96Nuclear pore
    • Protein or peptide: GATOR complex protein SEC13
    • Protein or peptide: Nuclear pore complex proteinNuclear pore
    • Protein or peptide: outer Nup133
    • Protein or peptide: MGC83295 protein
    • Protein or peptide: Protein ELYS
    • Protein or peptide: Nuclear pore complex protein Nup93Nuclear pore

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Supramolecule #1: nuclear pore complex

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

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Macromolecule #1: Nuclear pore complex protein Nup85

MacromoleculeName: Nuclear pore complex protein Nup85 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: African clawed frog (African clawed frog)
Molecular weightTheoretical: 75.160047 KDa
SequenceString: MEELDVDPAE TPIPGLGQQN RHIGFSWGPG DLLLYETLYQ KQGNSETAAR CPFMYLVRSD EDIYSPVLRK LFNESHSIFV GLQKSAEEA SGKSRKAQLV QVSRNYRSVL RACMEEMHTL SESTRETAQK YISQISILSA MELSWNLCEI LFIESAPAGP L LILLLEWV ...String:
MEELDVDPAE TPIPGLGQQN RHIGFSWGPG DLLLYETLYQ KQGNSETAAR CPFMYLVRSD EDIYSPVLRK LFNESHSIFV GLQKSAEEA SGKSRKAQLV QVSRNYRSVL RACMEEMHTL SESTRETAQK YISQISILSA MELSWNLCEI LFIESAPAGP L LILLLEWV RLHVCEVDNI VQDVLRSEKP TEHEKFWDGV TGYVLQGRMN EARQLLAKEA STSASARSMC RVLDDLLKKM PM LHTGGTQ TLTEFELKWQ HWREECERHL QNGTFSSNVH MEAVCRVLLG DEEVLLEKRD LMTTWYHFLV SRLLFKHPTV KPT ELHFYA QSSLDMFLAG DSCPEPLDNI LLAAFEFDIH QVIKEFSIVS SNWWFVAHLT DLLDHCQLFQ AHNLYFGANM REFL LLDYA SGLFSHHSLW QLGVDYFDYC PNLGREYLKL HMERIPLSTE KKALKALRIC EQRQMTEQVR SICKTMAMQS LCNRR LGSA LSWSIRAKDA AFATLISDRF LKEYCERGNF TDLDLIDNLG SAMLLSDRLT FLGKYREFHR MYSQEQFSEA ASLLLS LMT ARIAPCSFWL TLLLDALPLL EQKQVIFSAE QTYELMRCLE DRMAAKLEST SPDEIQKQDS SIDNTKVEML RLALARN LA RAIVTEGALQ E

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Macromolecule #2: MGC154553 protein

MacromoleculeName: MGC154553 protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: African clawed frog (African clawed frog)
Molecular weightTheoretical: 41.744512 KDa
SequenceString: MADKFAAKFV SHKISRTRWR PVSASSLQQP DVFATGSWDN EENKVCVWAT SDFGATSLDE EYQGDPKQLC DIKHPGDVMD MQFLDKERI VTGSSTGTVT IFRHHENNQT LSVNQRWEQA HYHVGSNMRA PCTAIVCSSP EIVSVGEDGR INCFRAESRD V LRTIDDAD ...String:
MADKFAAKFV SHKISRTRWR PVSASSLQQP DVFATGSWDN EENKVCVWAT SDFGATSLDE EYQGDPKQLC DIKHPGDVMD MQFLDKERI VTGSSTGTVT IFRHHENNQT LSVNQRWEQA HYHVGSNMRA PCTAIVCSSP EIVSVGEDGR INCFRAESRD V LRTIDDAD SSTMHGVTFL RTTEILTVNS VGQLKLWDLR KQGNDPTQIF SVTGERVPLH CVDRHPNQQH VVATGGQDGM LC IWDVRHG KMPMSLLNAH EAEMWEVHFH PSNPDHLFTC SEDGSLWHWD ASADSEKPTF LLGGRSTFNI SRSSIAPPNA NQS LACAWL STDPTKGQLE ITNLLPSSTL SVNSLDVLGQ NLVCGTDAEA IYVTRRLFS

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Macromolecule #3: Nucleoporin SEH1-A

MacromoleculeName: Nucleoporin SEH1-A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: African clawed frog (African clawed frog)
Molecular weightTheoretical: 39.777566 KDa
SequenceString: MFVARSIAAD HKDLIHDVSF DFHGRRMATC SSDQSVKVWD KSENGNWHCT ASWKTHSGSV WRVTWAHPEF GQVLASCSFD RTAAVWEEI VGESNDKLRG QSHWVKRTTL VDSRTSVTDV KFAPKHMGLM LATCSADGVV RIYEAPDVMN LSQWSLQHEI S CKLSCSCI ...String:
MFVARSIAAD HKDLIHDVSF DFHGRRMATC SSDQSVKVWD KSENGNWHCT ASWKTHSGSV WRVTWAHPEF GQVLASCSFD RTAAVWEEI VGESNDKLRG QSHWVKRTTL VDSRTSVTDV KFAPKHMGLM LATCSADGVV RIYEAPDVMN LSQWSLQHEI S CKLSCSCI SWNPSSSRAH SPMIAVGSDD SSPNIMGKVQ IYEYNENTRK YAKAETLMSV SDPVHDIAFA PNLGRSFHIL AV ATKDVRI FTMKPLRKEL SSSGGVTKFE IHTVAQFDNH NSQVWRVSWN ITGTVLASSG DDGTVRLWKA NYMDNWKCIG VLK GDGNPV GNSYQGFFGS SVGSAGQSLQ NSVNGTPSSG RKHS

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Macromolecule #4: Nup160

MacromoleculeName: Nup160 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: African clawed frog (African clawed frog)
Molecular weightTheoretical: 163.1035 KDa
SequenceString: MAAAESHMTS FQAEDWAGSN ILPMVQRAGG STRGIMAASV NLERSYMELI GAERETSRRN FRDLSLRPDV SLVIGGPKYS DCAGGYCYN ESGSLLSATR NRFIHWTSYA DTLELVELSL DINLLNNAVR LKILNCSILP GGVHICETQN NIIVLILTNQ T VHRLILPH ...String:
MAAAESHMTS FQAEDWAGSN ILPMVQRAGG STRGIMAASV NLERSYMELI GAERETSRRN FRDLSLRPDV SLVIGGPKYS DCAGGYCYN ESGSLLSATR NRFIHWTSYA DTLELVELSL DINLLNNAVR LKILNCSILP GGVHICETQN NIIVLILTNQ T VHRLILPH PSRMYRSEII SDSHIQSIFT DIGKTNFHDP NNTYVIPAIP GRAPNSTAST AWLSSDGEAL FALPSVSGGI LV IKMPPRD MEGLVTIAEL KQSSVMQRLL TGWMPSSIRG DPGPAHLPVS LAVHTLDHDS YLFALCQDHK LRMWSYKDQM CLM VADMLE YVPVSKDIRQ TAGTGHKLRL AYSDTLEILY LGVYLHTPRQ GQFCVFQLVC TESNRYSLEH TSSIFTNQET LIDF TFTLS SMNIWALWLD DDNQTVMKHI NFERNQAGHW NPVFVNPLPD DDLAIGDEQE PQEAYLECLF APGRFTIAAL QKAIQ ILRK GSGRVLDLSW EELKKEVTLT VEKEIQNAVV DYDVSQEEFR QINIENWCKF YTCCLQYQET LSRPLALVVH PNTNMV CLL RKGFLSFLAP CSSVEHLYLV PGEHLLTVDE SVICDDVDGA SDIVSLIQCL HMIADYITED MAYQMESACC HPQSPER VA EQILEDLIAN DIDNIMENIQ NKLQDIRNPI QAISFLLQNM DYETNMDMEQ SQHNVRLNLS TLYGSVTASS VVCQAIYK I SATRFLICRD LLILQHLLLR LGDMALVGAG QLLHSQQELI PRAAQLLLSY YMIRWGSQCL ACAVPVDLLE SNLQHLSVL ELSDSQVEKR RYTSGIQTIV ELFFEDVGRK HFPQVFAHLF IQSGSSQVHR SLNWADLIHR ITSYLLQLLW PSNPNFQFAE CLMRNCQYT QLQEYVRLLL PWCQVNVGSC HFMLAQCYLV AGEGHKALDC FSQAASEVER EDFLEKLIRV EEGESVSPRL Q YYNRVLRL LEDVGLPELV IQLATIAISE ASDDWRSQAA LRTRIFKHHL DMGHNSQAYD ALTQIPDTSR QLDCLRQLVV VL CERSQLQ DLVEFPYVNL HNEVVGIIES RARAVDLMTH NYYELLYAFH IYRHNYRKAG TVMFEYGMRL GREVRTLRGL QKQ VNSYLA CLNCLRLIRP EYAWIVQPVS GAVYERPGAS PKRNYDGESS AVPSSSQIEI LELRDLEKEY VLAQTRLTLA KHNP STAAI AGSSAAEEMV ALLVQAGLFD TAISLCQTFK LGLTSIFEGL ACKCIRLQQG GEAAQAEAWE WLAANQLATV ITTKE SSAT DEAWRLMISY LDKYESKNTL YHHCIINKLL SHGVPLPNWL INRYKAMDAA ELLRLYLKYD LLEEAAELVL EYVDAL LGK GHQYFGIQAP LSATSQLVWF PYSAIDHLRL ALGENENNQH NQAILGKLQR KMDEYFQKLK KATDDYKKIV QKPVRA

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Macromolecule #5: MGC83926 protein

MacromoleculeName: MGC83926 protein / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: African clawed frog (African clawed frog)
Molecular weightTheoretical: 36.588625 KDa
SequenceString: MKQDSASNAT YTVDCEDYVH VVEFNPFDSG EAGSLLAYGG ISYVVIASCR FQEEDSTVEG IEFKTLKTFH HGERVVAIAW SPETRCDAL LPLLRFATAA GDKKIRIFTS DFQDKNEYKV IEGHSGYIND LVFCSPEGTD IASVGDDHTC RIWDLDGKQI A MFILRSPG ...String:
MKQDSASNAT YTVDCEDYVH VVEFNPFDSG EAGSLLAYGG ISYVVIASCR FQEEDSTVEG IEFKTLKTFH HGERVVAIAW SPETRCDAL LPLLRFATAA GDKKIRIFTS DFQDKNEYKV IEGHSGYIND LVFCSPEGTD IASVGDDHTC RIWDLDGKQI A MFILRSPG MSVAWHPEGA FKLMVAEKTG TIRFYDLTTH QAILSLESVQ VPLMSADWCV RNTLRIGAVA GNDWIIWEMP RS SYPQDNK PAHADRARMF RWSKCNENVF ATTGYPGKMK SQIAIHHLAH PQPILIGTAP VGSGLSWHRR LPLCVVGGYR KLF FWLTEM

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Macromolecule #6: Nuclear pore complex protein Nup96

MacromoleculeName: Nuclear pore complex protein Nup96 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: African clawed frog (African clawed frog)
Molecular weightTheoretical: 104.742812 KDa
SequenceString: SKYGLQDSDE EDDQLNSAEA KKLKTAPVPP QGKQPPLQQA TLPGKVTPPP QSPAVDQLDR VMELDSDMAD ITQDQDLDSV AEEQDISEE QEPLSASSHI ASSLGINPHA LQVMKASLLL EEEDGEIMSR FSSFPSSMDP YPDVRSPRLF PSSHAKRPSS I GLLQSKFS ...String:
SKYGLQDSDE EDDQLNSAEA KKLKTAPVPP QGKQPPLQQA TLPGKVTPPP QSPAVDQLDR VMELDSDMAD ITQDQDLDSV AEEQDISEE QEPLSASSHI ASSLGINPHA LQVMKASLLL EEEDGEIMSR FSSFPSSMDP YPDVRSPRLF PSSHAKRPSS I GLLQSKFS APSMSRLSET VQGSHSPKIH PAAPWSVPAP LAPSFIMPGP APDTHLRTVG TRRQQELVPL EKSVTHGRGT LM IDMGLFM GRSFRVGWGP NWTLVHNGDK LSERLNAEED RDMDTIDYGF LPKPTSAKSL TESPFKVHVE KLSLEQKTKD LQS YLLPLE IELKNSTVDK SGPCPHFRPN PGVTAIHDYA GWVRNFSSEA AEVEAVVKQW GLTWTLCESL WGQLKELEAS LDEP NEYVK NLERRKAFSH WLAQTAQERI EEEVSLYGPE RHIEAVFSYL TGGRISDACR LAQKSGDHRL SLLLSQMVGS QEVRD LITL QLVDWNKLQV DHYIQEERLR VFCLLSGTPV WRSSDNRSIN VCSQLDWKRT LGIHLWYMLP PTATVAQALH MYEQAF QEQ EGGEPYACYP LPPYLEDCGF SFGDDPSAKF ISLQRDVCVH LLKLYSERQY DLCQLLDPSS ATPDPLDYRL SWHMWMV LQ ALNYTHLSGH RQGMLHASYA AQLENVGLWE WAIFVLLHIQ DPHVREAAVR ELLNRHCVVH DSPESLAKEN FLIQRLCL P AQWIHKAKAV RSRRDGDKHK EALYLLKSHQ WNQCHKLVTR HLAADAVINE NYRYLRGFLG ELARPEHCKH IQDWETAGK VYLDYISVIE MLNQIRQDEC SGGELEKLHT KVMSLCKWVE LIQCYSAKGR LAQSEMAKRV ANILRVVLSL QQPPESMSDS SSEPRVPLR LLAPHIGRLP MPEDYALEEL RGLTQSYLRE LICGS

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Macromolecule #7: GATOR complex protein SEC13

MacromoleculeName: GATOR complex protein SEC13 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: African clawed frog (African clawed frog)
Molecular weightTheoretical: 35.315285 KDa
SequenceString: MVSVINTVDT SHEDMIHDAQ MDYYGIRLAT CSSDRSVKIF DVKNGGQILI ADLRGHDGPV WQVAWAHPMY GNILASCSYD RKVIIWKEE NGTWEKTYEY TGHDSSVNSV CWAPHDFGLV LACGSSDGAI SILTFTGDGP WEVKKISNAH TIGCNAVSWA P SVIPGSLV ...String:
MVSVINTVDT SHEDMIHDAQ MDYYGIRLAT CSSDRSVKIF DVKNGGQILI ADLRGHDGPV WQVAWAHPMY GNILASCSYD RKVIIWKEE NGTWEKTYEY TGHDSSVNSV CWAPHDFGLV LACGSSDGAI SILTFTGDGP WEVKKISNAH TIGCNAVSWA P SVIPGSLV DQPSSQKPNY IKRFVSGGCD NLVKIWREED GQWKEDQKLE AHSDWVRDVA WAPSIGLPTS TIASCSQDGR VY IWTSDDA ATNCWTPKLL HKFNDVVWHV SWSITANILA VSGGDNKVTL WKESVDGQWA CISDVNKGQG AVSTVTEGQL NDQ

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Macromolecule #8: Nuclear pore complex protein

MacromoleculeName: Nuclear pore complex protein / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: African clawed frog (African clawed frog)
Molecular weightTheoretical: 105.398547 KDa
SequenceString: MDMLSPVVRE AEVSRAARRQ SSNRKNPADE SWSNATPTRG PSSRTTGQTL FRQHMTPQTW NSSRPPDVSA ILGTVGRSPR LLQTPGRLA NLSMMSNPDD SVWTTTFSPG RTGMYTTLDS PSFTEDITLS AVMLQEEDPG EAATMSMYPD FLKSFLEHPS S AVFELIEQ ...String:
MDMLSPVVRE AEVSRAARRQ SSNRKNPADE SWSNATPTRG PSSRTTGQTL FRQHMTPQTW NSSRPPDVSA ILGTVGRSPR LLQTPGRLA NLSMMSNPDD SVWTTTFSPG RTGMYTTLDS PSFTEDITLS AVMLQEEDPG EAATMSMYPD FLKSFLEHPS S AVFELIEQ YEATCNTQIT LLKKIVKRVT PGQQKFSKTA SILWLLQQEM VTWRLIAALY RDRIQSALEE ENMFEIAAPN AS EKTIVDK LFQRDTLVRQ SQLVVDWLES IAKDEVGDFS DNIEYYAKSV YWENTLHTLK QRSMLSLGSS RPLVSELDPD API RQKLPL DDLDREDDIR LLKYLFTLIR AGMTDEAQRL CKRCGQAWRA ATLEGWKLYH DANINGGTEL QAVEGNPYRC VWKT CCWRM AEDEQFNKYE RAIYATLSGN LKQLLPVCES WEDTVWAHFK VMVDSLVEQE IRASIISFNE ANELPREYLE ANWTL DSVF EELQATDKKR VLEENREHYH IIQKFVILAD VDGLMDEFSE WLSNGKNLLL GHLLRFMTHL LLFFRTLGLQ AKEEVS VEV LKTYIQRLIN EKQIELIAFY VSHLPQELAI SQYAVFLENI TDPDQRQRCL ELAKEAGLDV ASITKTVVEN TRKKDAG EF AHHDFAPALD SGTSEEDRAK IDVIDWLVFD PAQRAEALKQ SNAIMRKFLA SKKHEAAKEV FAKIPQDSIA EIYSQWEE Q AMDSALPAED DNAIREHLCI RAYLESHEAF NEWFKHINSP PQKPTLVGQA SFTEKVAHEH KEKKYEMDFG IWKGHLDAL TSDVKEKIYN VLLFVDGGWM VDVREDTEED PERSHQMVLL RRLCLPMMCF LLHTVLHNTK QYKDCLRLAD IVSSENQKLY TVFSKTEMR NLLQKLRESS LMLLDLQLDP LGYEIQS

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Macromolecule #9: outer Nup133

MacromoleculeName: outer Nup133 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: African clawed frog (African clawed frog)
Molecular weightTheoretical: 127.55125 KDa
SequenceString: MFPSPRAQGM GSARRPFNSR LTGGRKALGP GVTASSSPSA LYSPVGRRVS ASGARSTPSR VYLHPAASET VNYNVQLFGS SLPVKVMEA LSNASADEPM AACIHEGGWA WLACNDRLII WKISHSSSAK LMVCKELPLP LSDSEWSADL VDICAQTGDP A AAQSVALM ...String:
MFPSPRAQGM GSARRPFNSR LTGGRKALGP GVTASSSPSA LYSPVGRRVS ASGARSTPSR VYLHPAASET VNYNVQLFGS SLPVKVMEA LSNASADEPM AACIHEGGWA WLACNDRLII WKISHSSSAK LMVCKELPLP LSDSEWSADL VDICAQTGDP A AAQSVALM AATPEGSSRY WPNILHEGTY IESYTEFGSS LCAFVTAVKG NSFILSSEKN QLVRLTPDAS GKMNQRVLPQ GQ GMLSGIG RRVSTLFGIL SPAVESTLCS VLWDKGDCFY TLTDSSINKW DLDDTSESQV LNWDMSRVLR EYISDAIWGS ESD YDDIKA GININYLSLN QNCDGLVILS AAWHPGDNPC QIYYTLVTVK DEGYNISDEI TVEVTQFNPV FQARGMQLCQ LVVP NFSSQ ACYLYTQEMI FACSTGTGRS TLPQEKIPFE AQGDNIVGAG SCEGWPVFFI RKSGMLTVVA RETASVLPEH MEESL SSVS KSSRQAVVKD SRPDQIAHDD KTKHLKAAFL RYCRKDILGA QSMVDSLFSD SDMEPDDELD LAVNQISVDL IDDYPA SDP RWAESVPEEA AGFSNTSLIL LHQLEDKMKA HSFFVDFLHQ VGLFSRLSTC QTKGMLVATR LLLSEHAEKL SAAIVLK NH HAKLPVLVNS AIQLALDKRM CTVPQNLTAA DVYFREVSQM EIIFECLVDK EEADLESTSI DSVEWANIVV NVNTILKD M LHVACQYRQS KNSLYKNESG IQEPEHVPWT ASSGTAGIRS VVTRQHGIIL KVYPQADSGL RTILIEQLAA LLNYLLDDY VTQLKSIDKL ANEERYNILE MEYAQKRSEL LSPLLILGQY AWASNLAEKY CDFDILVQIC EMTDNQSRLQ RYMTLFAEQN FSDFLFRWY LEKGKRGKLL SQPASQHGQL AAFLQAHDHL SWLHELNSQE FEKAHRTLQT LANMETRYFC KKKTLLGLSK L AALASDFQ EDVLQEKVEE IAEQEHFLLH QETLPKKLLE EKQLDLNAMP VLAPFQLIQL YVCEENKRAN ENDFMKALDL LE YIGDDSE VDVEELKLEI LCKAIKRDEW SATDGKDDPI EATKDSIFVK VLQNLLNKGI ELKGYLPKAE TLLQSEELNS LKT NSYFEF SLKANYECYM KMQS

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Macromolecule #10: MGC83295 protein

MacromoleculeName: MGC83295 protein / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: African clawed frog (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

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Macromolecule #11: Protein ELYS

MacromoleculeName: Protein ELYS / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: African clawed frog (African clawed frog)
Molecular weightTheoretical: 268.771125 KDa
SequenceString: MQNLEAQVTG SLVAFPDVTQ KALKEDEINL DSVLRGKFST GRTSLAWLAC GPQLEITNSV TGERISAYHF SGLTERPPVV VAVKEFTWQ KKTGLLVGLV EAEGSVLCLY DIGISKVVKA VVLPGSVTAV EPIINHGGAS ASTQHLHQSL RWFFGVTAVV T DVGHVLLI ...String:
MQNLEAQVTG SLVAFPDVTQ KALKEDEINL DSVLRGKFST GRTSLAWLAC GPQLEITNSV TGERISAYHF SGLTERPPVV VAVKEFTWQ KKTGLLVGLV EAEGSVLCLY DIGISKVVKA VVLPGSVTAV EPIINHGGAS ASTQHLHQSL RWFFGVTAVV T DVGHVLLI DLCLDEVSSN QDELDASDLE VMSVIPTKIP KLREAATRER RHLCLQLAAP TGTTVSCLSY ISRTNQLAVG YS DGYFSLW NMKTLRRDYH VQIEGGRVPV CAVAFQEPEN DPRNCCYLWA VQSSESGGDV SLHLLQLAFS DRKCLASGQI MYE LLEYCE ERYSLDLSGS TLSLRGQSNN TKLLGCQTIE KFRVHGERED GVHEVTSPDT SVSVFSWQVN TYGQGKPSVY LGVF DINRW YQAQMPDSLR SGQFLRNCSY FAFWSLEAVV NITTQDIIFD ILVHERSLSR GIPPSYPPPE QFYYPSTYNF DATCL LNSG LIHFACTGFQ KETLHFLKKS GSSLNEAIPD GYNRCLAAGL LAPKFTDVQA SSLSQEEQLQ AILAAAVETS SLGLLT SCI KRWTAEEQPR SAANLRFVLE WTWKKVTLTK QEFDRLCFRL FDGSCNFIDP HTLQSLQQCH LYFSNLTAVL NCFIAQA KE VTQQGAVDLT NKQSVTRLLT LYASVVLWFC RSGMLPDSSD ETVQLTRPFY NYQVIQQYYS DQRKKLERLA RGKWDTSS L MIDGLINQFG DRIQQLWSRD DNGTGKYPPA NLHALLDVYL LENADEMSKH AITIYFLLDI MYSFPDKPDS SIESFPTAF FVPGSLIKLI QGFWLLDHND YQNSVDCILN PASSRVMSWQ HSQIIENLLC HGDSRQALRY LQVMKPVATT SKEVKLHMTV LLANRSILE AWNLQRLHSS RLNVEELLKH MYEMCQEMGL IEELLKLTFT DFEQGYLHKF LQTTGVQNQE LLLVHHLQRA N YISALQLN QSLKTNHLND CDRRLRERSG ARNAILDQYG KILPRVQRTL ASERAKPYSL PSLVWREVAR PKPLSTTAKQ AA PGSIITK ANFICNVLSK IKEVSTANEK REEYSPYQSM VSEEPTAPPL QDIDVPDAFF GTPINKSRRV SRLLDSVVHP VLM EPTPLT SSDTDNNQTP HKSPLLKTSS PLHSSLRRIA HMRSFAKASE FSLLETPLVV RKAKALAANT ASSGYTSITP QSIL RSSVR TTPLVSPSVS PGRSLTPPLR PKETKISFME LSFTRHAKAA HSSEGNLLAI SPVLRSSPDA VWSVKGKVAS FTQNT PVKK LDEIDASSSG IQEESQDEME VSKEISNISV RSEQASLEYH DAPTPEDLEN DEISGTTNSQ PQVNEVHHQM EDGQLT EKP AELALTEMQE EFIDSEEREI EYISAPLNGP NALECMTAVP DIYLEDASQC ILETPEGSSV SVTGEQECVS SAKDSES VI SIHDSDDAHS NLSENDQDSE EIEENNLRVP TTVTRCEEFD LIETKDLEVE LEEADSEKTN YKDIYPDATV QLGFTVES I EQRYTCELAD RRETPSETDE IEGEHFETEN NFSLVLEGDV TEEEILEPSS SKTDLELTRP PIAHQKLISE NRENIENCE TTEKIPANMS PLVDSDHESK TLETLPSEAD LSVAEKVLKG TEEKDVPPEV HSEVVLESKL VGNAMMSLDS SESQEVIISQ YDNVISIEK LEMTQEKMYG EKTEQINEGQ VSPNRDQSTL VKPLTPRRSI RKSSKPADSS TDIIGNITLP TTPKRGLKKA K ENVDTLKN SISVVPEEEL TLGTRRITRK ATLTALDNPE PLQIKEPPSG EDLQVQPSTP TRGRRGKVIT SDDLKEPPSG ED LQVQPST PTRGRRGRVI TSDDLREPPP GEDLQVQPST PTRGRRGRVI TSDDIKESPS VEDLQVQPST PTRGRRGKVI TSD DIKEPP SVEDLQVQPS TPTRGRKGKV ITSDDIKEPL SGEDLQVQPS TPTRGRKGKV ITSDDIKEPL SEEVLQEQPS TPTR GRRGR VITSDGKGYE CVEEKNALPL TPTRITRSKN ILEPEKGISQ IEPEKGISQI EPDKGLSQIE DTGETEHEVV TPRRG RRGK RVVNELVKHF ERNSSQPNIK ADTSPPVSPK KVSLRWTRTR SENQRINATE EQASKIQEDL SDTPRKRYKK SSNKMG FEE TTDTVTEGAI VEDVQESLII SHLGKNPNTS IVRSARKTAL PPVTEDHSEQ PLLPPESHSK VHSSLAIADE ENKTNTR TR SGNKSSVDVS AITFEFSTPK ARTKKTAKGS AVPTELIPST QYVFSPPSTR TRRATRANVS EAVIEPQLQF QESCEIAE T EVPEVPASKP RGRPPKHKAK AVTRVLKKPS WSTPPVEIKL ISPPESPAVS ETNTKTDSTE AKGAEKISVR RTRRRIIAK PVTRRKMR

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Macromolecule #12: Nuclear pore complex protein Nup93

MacromoleculeName: Nuclear pore complex protein Nup93 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: African clawed frog (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

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 6.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

3103

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 417490
FSC plot (resolution estimation)

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