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- EMDB-32643: Cryo-EM structure of full-length Nup188 -

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Basic information

Entry
Database: EMDB / ID: EMD-32643
TitleCryo-EM structure of full-length Nup188
Map data
Sample
  • Complex: Cryo-EM structure of full-length Nup188
    • Protein or peptide: Nucleoporin NUP188
Function / homology
Function and homology information


mRNA export from nucleus in response to heat stress / nuclear pore inner ring / nuclear pore organization / structural constituent of nuclear pore / RNA export from nucleus / nucleocytoplasmic transport / nuclear pore / protein import into nucleus / nuclear envelope / nuclear membrane
Similarity search - Function
Nuclear pore protein Nup188, C-terminal / Nuclear pore protein NUP188 C-terminal domain / Nucleoporin Nup188, N-terminal / Nucleoporin Nup188, N-terminal / : / Nucleoporin Nup188, N-terminal subdomain III / Nucleoporin Nup188
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsZhao L / Li ZQ / Sui SF
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Res / Year: 2022
Title: Near-atomic structure of the inner ring of the Saccharomyces cerevisiae nuclear pore complex.
Authors: Zongqiang Li / Shuaijiabin Chen / Liang Zhao / Guoqiang Huang / Xiong Pi / Shan Sun / Peiyi Wang / Sen-Fang Sui /
Abstract: Nuclear pore complexes (NPCs) mediate bidirectional nucleocytoplasmic transport of substances in eukaryotic cells. However, the accurate molecular arrangement of NPCs remains enigmatic owing to their ...Nuclear pore complexes (NPCs) mediate bidirectional nucleocytoplasmic transport of substances in eukaryotic cells. However, the accurate molecular arrangement of NPCs remains enigmatic owing to their huge size and highly dynamic nature. Here we determined the structure of the asymmetric unit of the inner ring (IR monomer) at 3.73 Å resolution by single-particle cryo-electron microscopy, and created an atomic model of the intact IR consisting of 192 molecules of 8 nucleoporins. In each IR monomer, the Z-shaped Nup188-Nup192 complex in the middle layer is sandwiched by two approximately parallel rhomboidal structures in the inner and outer layers, while Nup188, Nup192 and Nic96 link all subunits to constitute a relatively stable IR monomer. In contrast, the intact IR is assembled by loose and instable interactions between IR monomers. These structures, together with previously reported structural information of IR, reveal two distinct interaction modes between IR monomers and extensive flexible connections in IR assembly, providing a structural basis for the stability and malleability of IR.
History
DepositionJan 20, 2022-
Header (metadata) releaseMar 30, 2022-
Map releaseMar 30, 2022-
UpdateMay 18, 2022-
Current statusMay 18, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32643.png

Downloads & links

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Map

FileDownload / File: emd_32643.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.668 Å
Density
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-2.175091 - 3.0663555
Average (Standard dev.)-0.00026942365 (±0.045527335)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 320.63998 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of full-length Nup188

EntireName: Cryo-EM structure of full-length Nup188
Components
  • Complex: Cryo-EM structure of full-length Nup188
    • Protein or peptide: Nucleoporin NUP188

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Supramolecule #1: Cryo-EM structure of full-length Nup188

SupramoleculeName: Cryo-EM structure of full-length Nup188 / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)

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Macromolecule #1: Nucleoporin NUP188

MacromoleculeName: Nucleoporin NUP188 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (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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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: 3.0 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 607216
FSC plot (resolution estimation)

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