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Basic information

Entry
Database: PDB / ID: 7woo
TitleCryo-EM structure of the inner ring protomer of the Saccharomyces cerevisiae nuclear pore complex
Components
  • Nucleoporin NIC96
  • Nucleoporin NSP1
  • Nucleoporin NUP157
  • Nucleoporin NUP170
  • Nucleoporin NUP188
  • Nucleoporin NUP192
  • Nucleoporin NUP49/NSP49
  • Nucleoporin NUP57
KeywordsTRANSPORT PROTEIN / nuclear pore complex / inner ring / protomer / Saccharomyces cerevisiae
Function / homology
Function and homology information


nuclear pore linkers / : / 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 linkers / : / 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 / structural constituent of nuclear pore / RNA export from nucleus / poly(A)+ mRNA export from nucleus / nucleocytoplasmic transport / nuclear localization sequence binding / 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 / nuclear envelope / nuclear membrane / molecular adaptor activity / chromatin binding / protein-containing complex binding / DNA binding / RNA binding / identical protein binding / nucleus
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 Nup54/Nup57/Nup44 / Nucleoporin p58/p45 / Nucleoporin Nup54, alpha-helical domain / Nucleoporin Nup188 ...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 Nup54/Nup57/Nup44 / Nucleoporin p58/p45 / Nucleoporin Nup54, alpha-helical domain / Nucleoporin Nup188 / Nucleoporin complex subunit 54 / Nucleoporin, NSP1-like, C-terminal / Nucleoporin NSP1/NUP62 / Nsp1-like C-terminal region / Nucleoporin, Nup155-like / Nucleoporin, Nup155-like, C-terminal, subdomain 1 / Nucleoporin, Nup155-like, C-terminal, subdomain 2 / Nucleoporin Nup186/Nup192/Nup205 / Nuclear pore complex scaffold, nucleoporins 186/192/205 / Nucleoporin 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
Similarity search - Domain/homology
Nucleoporin NSP1 / Nucleoporin NIC96 / Nucleoporin NUP170 / Nucleoporin NUP157 / Nucleoporin NUP192 / Nucleoporin NUP57 / Nucleoporin NUP188 / Nucleoporin NUP49/NSP49
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.71 Å
AuthorsLi, Z.Q. / Chen, S.J.B. / Zhao, L. / Sui, S.F.
Funding support China, 1items
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 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoporin NIC96
C: Nucleoporin NUP157
D: Nucleoporin NUP170
E: Nucleoporin NUP188
F: Nucleoporin NUP192
G: Nucleoporin NUP49/NSP49
H: Nucleoporin NUP57
I: Nucleoporin NSP1
J: Nucleoporin NUP49/NSP49
K: Nucleoporin NUP57
L: Nucleoporin NSP1
Z: Nucleoporin NIC96


Theoretical massNumber of molelcules
Total (without water)1,286,20112
Polymers1,286,20112
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 8 types, 12 molecules AZCDEFGJHKIL

#1: Protein Nucleoporin NIC96 / 96 kDa nucleoporin-interacting component / Nuclear pore protein NIC96


Mass: 96291.586 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P34077
#2: Protein Nucleoporin NUP157 / Nuclear pore protein NUP157


Mass: 156827.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P40064
#3: Protein Nucleoporin NUP170 / Nuclear pore protein NUP170


Mass: 169651.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P38181
#4: Protein Nucleoporin NUP188 / Nuclear pore protein NUP188


Mass: 188753.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P52593
#5: Protein Nucleoporin NUP192 / Nuclear pore protein NUP192


Mass: 191718.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P47054
#6: Protein Nucleoporin NUP49/NSP49 / Nuclear pore protein NUP49/NSP49


Mass: 49174.762 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q02199
#7: Protein Nucleoporin NUP57 / Nuclear pore protein NUP57


Mass: 57547.145 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P48837
#8: Protein Nucleoporin NSP1 / Nuclear pore protein NSP1 / Nucleoskeletal-like protein / p110


Mass: 86611.672 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P14907

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of the inner ring protomer of the Saccharomyces cerevisiae nuclear pore complex
Type: COMPLEX / Entity ID: #4 / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.71 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1266268 / Symmetry type: POINT

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