+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12814 | |||||||||
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Title | In-cell human nuclear pore complex | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information positive regulation of mitotic cytokinetic process / GATOR2 complex / nephron development / centriole assembly / regulation of protein import into nucleus / positive regulation of centriole replication / Seh1-associated complex / regulation of Ras protein signal transduction / nuclear pore inner ring / protein localization to nuclear inner membrane ...positive regulation of mitotic cytokinetic process / GATOR2 complex / nephron development / centriole assembly / regulation of protein import into nucleus / positive regulation of centriole replication / Seh1-associated complex / regulation of Ras protein signal transduction / nuclear pore inner ring / protein localization to nuclear inner membrane / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear envelope organization / telomere tethering at nuclear periphery / nuclear pore central transport channel / COPII-coated vesicle cargo loading / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore organization / nuclear pore outer ring / nuclear pore complex assembly / atrial cardiac muscle cell action potential / somite development / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / COPII vesicle coat / positive regulation of protein localization to centrosome / Nuclear Pore Complex (NPC) Disassembly / paraxial mesoderm development / nuclear inclusion body / nuclear pore nuclear basket / Amino acids regulate mTORC1 / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / miRNA processing / Transport of the SLBP independent Mature mRNA / attachment of mitotic spindle microtubules to kinetochore / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / protein-containing complex localization / Transport of Mature mRNA Derived from an Intronless Transcript / negative regulation of Ras protein signal transduction / structural constituent of nuclear pore / Rev-mediated nuclear export of HIV RNA / SUMOylation of RNA binding proteins / Flemming body / Nuclear import of Rev protein / Transport of Mature mRNA derived from an Intron-Containing Transcript / negative regulation of programmed cell death / NEP/NS2 Interacts with the Cellular Export Machinery / RNA export from nucleus / tRNA processing in the nucleus / mitotic centrosome separation / centrosome cycle / positive regulation of mRNA splicing, via spliceosome / Postmitotic nuclear pore complex (NPC) reformation / neural tube development / COPII-mediated vesicle transport / nucleocytoplasmic transport / lamellipodium assembly / Viral Messenger RNA Synthesis / positive regulation of epidermal growth factor receptor signaling pathway / nuclear localization sequence binding / PTB domain binding / poly(A)+ mRNA export from nucleus / mitotic metaphase chromosome alignment / NLS-bearing protein import into nucleus / female gonad development / SUMOylation of ubiquitinylation proteins / negative regulation of epidermal growth factor receptor signaling pathway / Vpr-mediated nuclear import of PICs / macrophage chemotaxis / positive regulation of SMAD protein signal transduction / SUMOylation of DNA replication proteins / cellular response to nutrient levels / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / Regulation of HSF1-mediated heat shock response / positive regulation of TOR signaling / regulation of signal transduction / mRNA transport / protein targeting / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / nuclear pore / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / regulation of mitotic spindle organization / negative regulation of TORC1 signaling / Resolution of Sister Chromatid Cohesion / positive regulation of TORC1 signaling / Hsp70 protein binding / MHC class II antigen presentation / cellular response to amino acid starvation / serine-type peptidase activity / SH2 domain binding / SUMOylation of chromatin organization proteins / nuclear periphery / positive regulation of mitotic nuclear division Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 35.0 Å | |||||||||
Authors | Schuller AP / Wojtynek M / Schwartz TU / Medalia O / Weis K | |||||||||
Funding support | United States, Switzerland, 2 items
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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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12814.map.gz | 16.2 MB | EMDB map data format | |
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Header (meta data) | emd-12814-v30.xml emd-12814.xml | 9.6 KB 9.6 KB | Display Display | EMDB header |
Images | emd_12814.png | 60.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12814 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12814 | HTTPS FTP |
-Related structure data
Related structure data | 7peqMC 7perMC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | |
EM raw data | 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]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12814.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 6.84 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : In-cell human nuclear pore complex
Entire | Name: In-cell human nuclear pore complex |
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Components |
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-Supramolecule #1: In-cell human nuclear pore complex
Supramolecule | Name: In-cell human nuclear pore complex / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) / Strain: DLD-1 / Organelle: Nuclear envelope / Location in cell: Nuclear envelope |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 / Details: PBS |
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Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER |
Details | Cryo-FIB lamella |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 26000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.4 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Extraction | Number tomograms: 54 / Number images used: 1552 |
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Final angle assignment | Type: OTHER |
Final reconstruction | Applied symmetry - Point group: C8 (8 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 35.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 1254 |