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

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Basic information

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


GATOR2 complex / nephron development / 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 exit from endoplasmic reticulum / COPII-coated vesicle budding ...GATOR2 complex / nephron development / 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 exit from endoplasmic reticulum / COPII-coated vesicle budding / protein localization to nuclear inner membrane / nuclear pore inner ring / nuclear envelope organization / nuclear pore central transport channel / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / COPII-coated vesicle cargo loading / nuclear pore outer ring / nuclear pore complex assembly / telomere tethering at nuclear periphery / nuclear pore organization / atrial cardiac muscle cell action potential / somite development / COPII vesicle coat / positive regulation of protein localization to centrosome / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / paraxial mesoderm development / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / Amino acids regulate mTORC1 / Transport of Ribonucleoproteins into the Host Nucleus / nuclear pore nuclear basket / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / miRNA processing / attachment of mitotic spindle microtubules to kinetochore / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / negative regulation of Ras protein signal transduction / NLS-bearing protein import into nucleus / protein-containing complex localization / Transport of Mature mRNA Derived from an Intronless Transcript / structural constituent of nuclear pore / nuclear localization sequence binding / positive regulation of mRNA splicing, via spliceosome / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / Flemming body / SUMOylation of RNA binding proteins / mitotic centrosome separation / NEP/NS2 Interacts with the Cellular Export Machinery / Transport of Mature mRNA derived from an Intron-Containing Transcript / centrosome cycle / tRNA processing in the nucleus / RNA export from nucleus / Postmitotic nuclear pore complex (NPC) reformation / COPII-mediated vesicle transport / negative regulation of programmed cell death / lamellipodium assembly / neural tube development / nucleocytoplasmic transport / positive regulation of epidermal growth factor receptor signaling pathway / Viral Messenger RNA Synthesis / poly(A)+ mRNA export from nucleus / PTB domain binding / mitotic metaphase chromosome alignment / SUMOylation of ubiquitinylation proteins / female gonad development / Vpr-mediated nuclear import of PICs / negative regulation of epidermal growth factor receptor signaling pathway / macrophage chemotaxis / 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 / cellular response to nutrient levels / nuclear pore / protein targeting / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / negative regulation of TORC1 signaling / neurogenesis / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / positive regulation of TORC1 signaling / serine-type peptidase activity / Hsp70 protein binding / MHC class II antigen presentation / positive regulation of mitotic nuclear division / regulation of mitotic spindle organization / SH2 domain binding / Resolution of Sister Chromatid Cohesion / cellular response to amino acid starvation / nuclear periphery
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 Nup120/160, beta-propeller domain ...: / : / : / 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 Nup120/160, beta-propeller domain / Nucleoporin p58/p45 / Nucleoporin Nup37 / Nucleoporin, Nup155-like, C-terminal, subdomain 3 / 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 / 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 peptidase S59-like / Nup98-96 autopeptidase S59 / NUP C-terminal domain profile. / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / 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: 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
  • Download
  • Surface view colored by height
  • Surface level: 1.45E-6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12813.png

Downloads & links

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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)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.84 Å/pix.
x 100 pix.
= 684. Å		6.84 Å/pix.
x 100 pix.
= 684. Å		6.84 Å/pix.
x 100 pix.
= 684. 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: 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
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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
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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 39.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 1252
ExtractionNumber tomograms: 54 / Number images used: 1552
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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