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- EMDB-12813: Segment of the nucleoplasmic ring of the human nuclear pore complex -

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Entry
Database: EMDB / ID: EMD-12813
TitleSegment 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


positive regulation of mitotic cytokinetic process / GATOR2 complex / nephron development / centriole assembly / regulation of protein import into nucleus / positive regulation of centriole replication / nuclear pore inner ring / Seh1-associated complex / protein localization to nuclear inner membrane / regulation of Ras protein signal transduction ...positive regulation of mitotic cytokinetic process / GATOR2 complex / nephron development / centriole assembly / regulation of protein import into nucleus / positive regulation of centriole replication / nuclear pore inner ring / Seh1-associated complex / protein localization to nuclear inner membrane / regulation of Ras protein signal transduction / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear envelope organization / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore central transport channel / telomere tethering at nuclear periphery / COPII-coated vesicle cargo loading / nuclear pore organization / nuclear pore complex assembly / nuclear pore outer ring / atrial cardiac muscle cell action potential / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / somite development / COPII vesicle coat / Nuclear Pore Complex (NPC) Disassembly / positive regulation of protein localization to centrosome / nuclear inclusion body / nuclear pore nuclear basket / paraxial mesoderm development / 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 / Transport of the SLBP Dependant Mature mRNA / negative regulation of Ras protein signal transduction / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / protein-containing complex localization / Transport of Mature mRNA Derived from an Intronless Transcript / RNA export from nucleus / positive regulation of mRNA splicing, via spliceosome / structural constituent of nuclear pore / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / Flemming body / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / negative regulation of programmed cell death / mitotic centrosome separation / centrosome cycle / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / neural tube development / COPII-mediated vesicle transport / poly(A)+ mRNA export from nucleus / lamellipodium assembly / Viral Messenger RNA Synthesis / nuclear localization sequence binding / positive regulation of epidermal growth factor receptor signaling pathway / PTB domain binding / NLS-bearing protein import into nucleus / mitotic metaphase chromosome alignment / macrophage chemotaxis / female gonad development / negative regulation of epidermal growth factor receptor signaling pathway / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / cellular response to nutrient levels / positive regulation of SMAD protein signal transduction / SUMOylation of DNA replication proteins / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of TOR signaling / Regulation of HSF1-mediated heat shock response / protein targeting / mRNA transport / regulation of signal transduction / 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 / regulation of mitotic spindle organization / EML4 and NUDC in mitotic spindle formation / negative regulation of TORC1 signaling / Hsp70 protein binding / Resolution of Sister Chromatid Cohesion / positive regulation of TORC1 signaling / cellular response to amino acid starvation / MHC class II antigen presentation / SH2 domain binding / nuclear periphery / serine-type peptidase activity / SUMOylation of chromatin organization proteins / neurogenesis
Similarity search - Function
Nucleoporin FG repeated region / Nup54, C-terminal interacting domain / Nup54 C-terminal interacting domain / Nucleoporin Nup120/160 / Nup98, Gle2-binding sequence / Nucleoporin p58/p45 / Nucleoporin, Nup155-like, C-terminal, subdomain 3 / Nucleoporin, NSP1-like, C-terminal / Nucleoporin Nup54/Nup57/Nup44 / Nucleoporin Nup54, alpha-helical domain ...Nucleoporin FG repeated region / Nup54, C-terminal interacting domain / Nup54 C-terminal interacting domain / Nucleoporin Nup120/160 / Nup98, Gle2-binding sequence / Nucleoporin p58/p45 / Nucleoporin, Nup155-like, C-terminal, subdomain 3 / Nucleoporin, NSP1-like, C-terminal / Nucleoporin Nup54/Nup57/Nup44 / Nucleoporin Nup54, alpha-helical domain / Nucleoporin NSP1/NUP62 / Nucleoporin Nup37 / Nsp1-like C-terminal region / Nucleoporin complex subunit 54 / 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 / Non-repetitive/WGA-negative nucleoporin C-terminal / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like / Sec13/Seh1 family / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / 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. / Nucleoporin peptidase S59-like / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / 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: 39.0 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: 1.45E-6
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 1.45E-6
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12813.png

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Map

FileDownload / File: emd_12813.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 6.84 Å
Density
Contour LevelBy AUTHOR: 1.45e-06 / Movie #1: 1.5E-6
Minimum - Maximum-1.4878461e-06 - 1.0799352e-05
Average (Standard dev.)8.63231e-08 (±6.094479e-07)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 684.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.846.846.84
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z684.000684.000684.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ260260260
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.0000.0000.000

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Supplemental data

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Mask #1

Fileemd_12813_msk_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_12813_half_map_1.map
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Half map: #2

Fileemd_12813_half_map_2.map
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Sample components

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Entire : Segment of the nucleoplasmic ring of the human nuclear pore complex

EntireName: Segment of the nucleoplasmic ring of the human nuclear pore complex
Components
  • Complex: Segment of the nucleoplasmic ring of the human nuclear pore complex

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Supramolecule #1: Segment of the nucleoplasmic ring of the human nuclear pore complex

SupramoleculeName: Segment of the nucleoplasmic ring of the 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 stageCooling holder cryogen: NITROGEN
Image recordingFilm 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

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Image processing

ExtractionNumber tomograms: 54 / Number images used: 1552
Final angle assignmentType: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 39.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 1252
FSC plot (resolution estimation)

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