- EMDB-12813: Segment of the nucleoplasmic ring of the human nuclear pore complex -
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Entry
Database: EMDB / ID: EMD-12813
Title
Segment of the nucleoplasmic ring of the human nuclear pore complex
Map data
Sample
Complex: Segment of the nucleoplasmic ring of the human nuclear pore complex
Function / homology
Function and homology information
nephron development / GATOR2 complex / centriole assembly / positive regulation of centriole replication / regulation of protein import into nucleus / regulation of Ras protein signal transduction / positive regulation of mitotic cytokinetic process / Seh1-associated complex / protein localization to nuclear inner membrane / nuclear pore inner ring ...nephron development / GATOR2 complex / centriole assembly / positive regulation of centriole replication / regulation of protein import into nucleus / regulation of Ras protein signal transduction / positive regulation of mitotic cytokinetic process / Seh1-associated complex / protein localization to nuclear inner membrane / nuclear pore inner ring / nuclear envelope organization / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear pore central transport channel / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / COPII-coated vesicle cargo loading / nuclear pore complex assembly / telomere tethering at nuclear periphery / nuclear pore outer ring / nuclear pore organization / atrial cardiac muscle cell action potential / somite development / nuclear pore cytoplasmic filaments / COPII vesicle coat / positive regulation of protein localization to centrosome / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / female gonad development / paraxial mesoderm development / nuclear inclusion body / Nuclear Pore Complex (NPC) Disassembly / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Amino acids regulate mTORC1 / miRNA processing / attachment of mitotic spindle microtubules to kinetochore / Transport of the SLBP independent Mature mRNA / NS1 Mediated Effects on Host Pathways / Transport of the SLBP Dependant Mature mRNA / negative regulation of Ras protein signal transduction / NLS-bearing protein import into nucleus / SUMOylation of SUMOylation proteins / protein-containing complex localization / structural constituent of nuclear pore / nuclear localization sequence binding / Transport of Mature mRNA Derived from an Intronless Transcript / positive regulation of mRNA splicing, via spliceosome / Rev-mediated nuclear export of HIV RNA / Flemming body / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / mitotic centrosome separation / NEP/NS2 Interacts with the Cellular Export Machinery / centrosome cycle / RNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / COPII-mediated vesicle transport / negative regulation of programmed cell death / lamellipodium assembly / nucleocytoplasmic transport / neural tube development / positive regulation of epidermal growth factor receptor signaling pathway / poly(A)+ mRNA export from nucleus / Viral Messenger RNA Synthesis / PTB domain binding / mitotic metaphase chromosome alignment / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / macrophage chemotaxis / negative regulation of epidermal growth factor receptor signaling pathway / SUMOylation of DNA replication proteins / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of SMAD protein signal transduction / positive regulation of TOR signaling / Regulation of HSF1-mediated heat shock response / mRNA transport / regulation of signal transduction / nuclear pore / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / cellular response to nutrient levels / negative regulation of TORC1 signaling / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / neurogenesis / Hsp70 protein binding / positive regulation of TORC1 signaling / serine-type peptidase activity / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / positive regulation of mitotic nuclear division / MHC class II antigen presentation / SH2 domain binding / nuclear periphery / cellular response to amino acid starvation / regulation of mitotic spindle organization / Resolution of Sister Chromatid Cohesion / SUMOylation of chromatin organization proteins Similarity search - Function
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
R01-GM77537
United States
Swiss National Science Foundation
SNSF 31003A_179418
Switzerland
Citation
Journal: Nature / Year: 2021 Title: The cellular environment shapes the nuclear pore complex architecture. Authors: Anthony P Schuller / Matthias Wojtynek / David Mankus / Meltem Tatli / Rafael Kronenberg-Tenga / Saroj G Regmi / Phat V Dip / Abigail K R Lytton-Jean / Edward J Brignole / Mary Dasso / ...Authors: Anthony P Schuller / Matthias Wojtynek / David Mankus / Meltem Tatli / Rafael Kronenberg-Tenga / Saroj G Regmi / Phat V Dip / Abigail K R Lytton-Jean / Edward J Brignole / Mary Dasso / Karsten Weis / Ohad Medalia / Thomas U Schwartz / Abstract: Nuclear pore complexes (NPCs) create large conduits for cargo transport between the nucleus and cytoplasm across the nuclear envelope (NE). These multi-megadalton structures are composed of about ...Nuclear pore complexes (NPCs) create large conduits for cargo transport between the nucleus and cytoplasm across the nuclear envelope (NE). These multi-megadalton structures are composed of about thirty different nucleoporins that are distributed in three main substructures (the inner, cytoplasmic and nucleoplasmic rings) around the central transport channel. Here we use cryo-electron tomography on DLD-1 cells that were prepared using cryo-focused-ion-beam milling to generate a structural model for the human NPC in its native environment. We show that-compared with previous human NPC models obtained from purified NEs-the inner ring in our model is substantially wider; the volume of the central channel is increased by 75% and the nucleoplasmic and cytoplasmic rings are reorganized. Moreover, the NPC membrane exhibits asymmetry around the inner-ring complex. Using targeted degradation of Nup96, a scaffold nucleoporin of the cytoplasmic and nucleoplasmic rings, we observe the interdependence of each ring in modulating the central channel and maintaining membrane asymmetry. Our findings highlight the inherent flexibility of the NPC and suggest that the cellular environment has a considerable influence on NPC dimensions and architecture.
History
Deposition
Apr 28, 2021
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Header (metadata) release
Oct 20, 2021
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Map release
Oct 20, 2021
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Update
Nov 24, 2021
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Current status
Nov 24, 2021
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
EMPIAR-10700 (Title: Cryo electron tomography of FIB-milled lamella of human DLD-1 cells Data size: 8.0 Data #1: Un-aligned tilt series of FIB-lamella of human DLD-1 cells [tilt series]) EMPIAR-10701 (Title: Cryo electron tomography of FIB-milled lamella of human DLD-1 cells Data size: 8.0 Data #1: Un-aligned tilt series of FIB-milled lamella of Nup96-depleted human DLD-1 cells [tilt series])
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