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 / : / regulation of protein desumoylation / peroxisomal importomer complex / mRNA export from nucleus in response to heat stress / Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / protein exit from endoplasmic reticulum / protein localization to nuclear inner membrane / COPII-mediated vesicle transport / COPII-coated vesicle budding / nuclear pore inner ring / nuclear pore localization / adenyl-nucleotide exchange factor activity / regulation of nucleocytoplasmic transport / regulation of TORC1 signaling / establishment of mitotic spindle localization / nuclear pore central transport channel / nuclear migration along microtubule / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / telomere tethering at nuclear periphery / nuclear pore outer ring / nuclear pore complex assembly / nuclear pore organization / tRNA export from nucleus / COPII vesicle coat / nuclear pore cytoplasmic filaments / positive regulation of protein exit from endoplasmic reticulum / Transport of Mature mRNA derived from an Intron-Containing Transcript / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Regulation of HSF1-mediated heat shock response / nuclear pore nuclear basket / SUMOylation of SUMOylation proteins / cytoplasmic dynein complex / protein localization to kinetochore / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / RNA export from nucleus / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport / silent mating-type cassette heterochromatin formation / vacuolar membrane / regulation of mitotic nuclear division / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / 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 / ribosomal small subunit export from nucleus / mRNA export from nucleus / heterochromatin formation / nuclear pore / ERAD pathway / positive regulation of TORC1 signaling / Neutrophil degranulation / cellular response to amino acid starvation / protein export from nucleus / nuclear periphery / molecular condensate scaffold activity / chromosome segregation / cell periphery / promoter-specific chromatin binding / phospholipid binding / protein import into nucleus / transcription corepressor activity / double-strand break repair / protein transport / nuclear envelope / single-stranded DNA binding / nuclear membrane / amyloid fibril formation / chromosome, telomeric region / hydrolase activity / cell cycle / cell division / chromatin binding / protein-containing complex binding / endoplasmic reticulum membrane / structural molecule activity / positive regulation of DNA-templated transcription / 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 / cytoplasm / cytosol

Domain/homology:

Nucleoporin Nup159/Nup146, N-terminal / Nucleoporin or Nuclear pore complex subunit NUP214=Nup159 / 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 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 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 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 / 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 / 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. / Dynein light chain, type 1/2 / Dynein light chain superfamily / Nucleoporin peptidase S59-like / Dynein light chain type 1 / 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