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- EMDB-12814: In-cell human nuclear pore complex -

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Basic information

Entry
Database: EMDB / ID: EMD-12814
TitleIn-cell human nuclear pore complex
Map data
Sample
  • Complex: In-cell 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
: / : / : / Nucleoporin NUP160, helical domain / Nup160 C-terminal TPR / NUP160/120 middle TPR / Nucleoporin FG repeated region / Nup54, C-terminal interacting domain / Nup54 C-terminal interacting domain / Nucleoporin p58/p45 ...: / : / : / Nucleoporin NUP160, helical domain / Nup160 C-terminal TPR / NUP160/120 middle TPR / Nucleoporin FG repeated region / Nup54, C-terminal interacting domain / Nup54 C-terminal interacting domain / Nucleoporin p58/p45 / Nucleoporin Nup37 / Nucleoporin, Nup155-like, C-terminal, subdomain 3 / Nucleoporin Nup120/160, beta-propeller domain / Nucleoporin Nup54/Nup57/Nup44 / Nucleoporin Nup54, alpha-helical domain / 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 / Nup98, Gle2-binding sequence / Nuclear pore protein 84/107 / Nuclear pore protein 84 / 107 / Nuclear pore complex protein Nup133-like / Nucleoporin, Nup155-like, C-terminal, subdomain 1 / Nucleoporin, Nup155-like, C-terminal, subdomain 2 / Nucleoporin, Nup155-like / Nucleoporin Nup186/Nup192/Nup205 / Nuclear pore complex scaffold, nucleoporins 186/192/205 / Nucleoporin, Nup133/Nup155-like, C-terminal / Non-repetitive/WGA-negative nucleoporin C-terminal / Nucleoporin interacting component Nup93/Nic96 / Nup93/Nic96 / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Sec13/Seh1 family / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin peptidase S59-like / Nup98-96 autopeptidase S59 / NUP C-terminal domain profile. / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Nuclear pore complex protein Nup155 / Nuclear pore glycoprotein p62 / Nuclear pore complex protein Nup98-Nup96 / Protein SEC13 homolog / Nuclear pore complex protein Nup107 / Nuclear pore complex protein Nup160 / Nucleoporin p54 / Nuclear pore complex protein Nup93 / Nucleoporin Nup43 / Nucleoporin Nup37 ...Nuclear pore complex protein Nup155 / Nuclear pore glycoprotein p62 / Nuclear pore complex protein Nup98-Nup96 / Protein SEC13 homolog / Nuclear pore complex protein Nup107 / Nuclear pore complex protein Nup160 / Nucleoporin p54 / Nuclear pore complex protein Nup93 / Nucleoporin Nup43 / Nucleoporin Nup37 / Nuclear pore complex protein Nup133 / Nuclear pore complex protein Nup205 / Nucleoporin SEH1 / Nucleoporin p58/p45 / Nuclear pore complex protein Nup85
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 35.0 Å
AuthorsSchuller AP / Wojtynek M / Schwartz TU / Medalia O / Weis K
Funding support United States, Switzerland, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM77537 United States
Swiss National Science FoundationSNSF 31003A_179418 Switzerland
CitationJournal: 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
DepositionApr 28, 2021-
Header (metadata) releaseOct 20, 2021-
Map releaseOct 20, 2021-
UpdateNov 24, 2021-
Current statusNov 24, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.44
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.44
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7peq
  • Surface level: 0.44
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7per
  • Surface level: 0.44
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7peq
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7per
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12814.png

Downloads & links

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Map

FileDownload / File: emd_12814.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.84 Å/pix.
x 320 pix.
= 2188.8 Å		6.84 Å/pix.
x 320 pix.
= 2188.8 Å		6.84 Å/pix.
x 320 pix.
= 2188.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.44 / Movie #1: 0.44
Minimum - Maximum0.0 - 1.0
Average (Standard dev.)0.3512861 (±0.04977975)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 2188.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.846.846.84
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z2188.8002188.8002188.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ260260260
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean0.0001.0000.351

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Supplemental data

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Sample components

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Entire : In-cell human nuclear pore complex

EntireName: In-cell human nuclear pore complex
Components
  • Complex: In-cell human nuclear pore complex

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Supramolecule #1: In-cell human nuclear pore complex

SupramoleculeName: In-cell human nuclear pore complex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human) / Strain: DLD-1 / Organelle: Nuclear envelope / Location in cell: Nuclear envelope

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4 / Details: PBS
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
DetailsCryo-FIB lamella

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 26000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied 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
ExtractionNumber tomograms: 54 / Number images used: 1552
Final angle assignmentType: OTHER

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