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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
SampleSegment 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 / nuclear pore inner ring / positive regulation of centriole replication / centriole assembly / protein localization to nuclear inner membrane / Seh1-associated complex / regulation of protein import into nucleus / protein exit from endoplasmic reticulum ...positive regulation of mitotic cytokinetic process / GATOR2 complex / nephron development / nuclear pore inner ring / positive regulation of centriole replication / centriole assembly / protein localization to nuclear inner membrane / Seh1-associated complex / regulation of protein import into nucleus / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / atrial cardiac muscle cell action potential / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / annulate lamellae / nuclear pore complex assembly / regulation of Ras protein signal transduction / nuclear pore organization / transporter activity / nuclear pore central transport channel / paraxial mesoderm development / nuclear envelope organization / nuclear pore outer ring / COPII-coated vesicle cargo loading / posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery / attachment of mitotic spindle microtubules to kinetochore / COPII vesicle coat / Nuclear Pore Complex (NPC) Disassembly / nuclear pore nuclear basket / nuclear inclusion body / somite development / positive regulation of TORC1 signaling / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / protein-containing complex localization => GO:0031503 / positive regulation of protein localization to centrosome / Amino acids regulate mTORC1 / Transport of the SLBP independent Mature mRNA / nucleocytoplasmic transport / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / tRNA export from nucleus / Transport of Mature mRNA Derived from an Intronless Transcript / positive regulation of mRNA splicing, via spliceosome / SUMOylation of SUMOylation proteins / mitotic nuclear membrane reassembly / structural constituent of nuclear pore / negative regulation of Ras protein signal transduction / Flemming body / Rev-mediated nuclear export of HIV RNA / macrophage chemotaxis / Transport of Mature mRNA derived from an Intron-Containing Transcript / Nuclear import of Rev protein / tRNA processing in the nucleus / SUMOylation of RNA binding proteins / centrosome cycle / snRNP Assembly / NEP/NS2 Interacts with the Cellular Export Machinery / neural tube development / Viral Messenger RNA Synthesis / cell death / regulation of glycolytic process / COPII-mediated vesicle transport / kinetochore => GO:0000776 / PTB domain binding / NLS-bearing protein import into nucleus / signaling receptor complex adaptor activity / positive regulation of TOR signaling / Postmitotic nuclear pore complex (NPC) reformation / RNA export from nucleus / mitotic metaphase plate congression / poly(A)+ mRNA export from nucleus / positive regulation of epidermal growth factor receptor signaling pathway / negative regulation of programmed cell death / lamellipodium assembly / mitotic centrosome separation / nuclear localization sequence binding / neurogenesis / kinesin binding / SMAD protein signal transduction / regulation of gene silencing by miRNA / positive regulation of SMAD protein signal transduction / regulation of mitotic spindle organization / female gonad development / SUMOylation of ubiquitinylation proteins / protein sumoylation / intracellular transport of virus / Vpr-mediated nuclear import of PICs / protein targeting / SUMOylation of DNA replication proteins / regulation of signal transduction / nuclear pore / negative regulation of epidermal growth factor receptor signaling pathway / mRNA transport / host cell / Regulation of HSF1-mediated heat shock response / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation
Similarity search - Function
Nuclear pore glycoprotein p62, metazoa / Nsp1-like C-terminal region / Nucleoporin NSP1/NUP62 / Nucleoporin, NSP1-like, C-terminal / Nup93/Nic96 / Nucleoporin interacting component Nup93/Nic96 / Nucleoporin p58/p45 / Nucleoporin, Nup155-like, C-terminal, subdomain 3 / Nup54 C-terminal interacting domain / Nup54, C-terminal interacting domain ...Nuclear pore glycoprotein p62, metazoa / Nsp1-like C-terminal region / Nucleoporin NSP1/NUP62 / Nucleoporin, NSP1-like, C-terminal / Nup93/Nic96 / Nucleoporin interacting component Nup93/Nic96 / Nucleoporin p58/p45 / Nucleoporin, Nup155-like, C-terminal, subdomain 3 / Nup54 C-terminal interacting domain / Nup54, C-terminal interacting domain / Nucleoporin Nup186/Nup192/Nup205 / Nucleoporin Nup85-like / Nuclear pore complex scaffold, nucleoporins 186/192/205 / Nup85 Nucleoporin / Nucleoporin, Nup155-like, C-terminal, subdomain 1 / Nucleoporin, Nup155-like / Nucleoporin complex subunit 54 / Nuclear pore protein 84 / 107 / Nucleoporin, Nup155-like, C-terminal, subdomain 2 / Nucleoporin Nup54, alpha-helical domain / Nuclear pore protein 84/107 / Nucleoporin Nup37 / Nucleoporin Seh1 / Nuclear pore complex protein Nup133-like / Nucleoporin Nup54/Nup57/Nup44 / Nucleoporin Nup120/160 / Non-repetitive/WGA-negative nucleoporin C-terminal / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like / Nucleoporin, Nup133/Nup155-like, C-terminal / Nuclear protein 96 / Nuclear protein 96 / Protein Sec13 / Nuclear pore complex protein NUP98-NUP96 / NUP C-terminal domain profile. / Peptidase S59, nucleoporin superfamily / Peptidase S59, nucleoporin / Nucleoporin autopeptidase / Nucleoporin peptidase S59-like / Sec13/Seh1 family / : / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Nucleoporin Nup43 / Nucleoporin p58/p45 / Nucleoporin SEH1 / Nuclear pore complex protein Nup205 / Nuclear pore complex protein Nup133 / Nucleoporin Nup37 / Nuclear pore complex protein Nup107 / Nuclear pore complex protein Nup93 / Nucleoporin p54 / Nuclear pore complex protein Nup160 ...Nucleoporin Nup43 / Nucleoporin p58/p45 / Nucleoporin SEH1 / Nuclear pore complex protein Nup205 / Nuclear pore complex protein Nup133 / Nucleoporin Nup37 / Nuclear pore complex protein Nup107 / Nuclear pore complex protein Nup93 / Nucleoporin p54 / Nuclear pore complex protein Nup160 / Protein SEC13 homolog / Nuclear pore complex protein Nup98-Nup96 / Nuclear pore glycoprotein p62 / Nuclear pore complex protein Nup155 / Nuclear pore complex protein Nup85
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 39 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

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

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Slices (1/2)

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Images are generated by Spider.

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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Segmentation: #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
Number of Components: 1

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Component #1: protein, Segment of the nucleoplasmic ring of the human nuclear p...

ProteinName: Segment of the nucleoplasmic ring of the human nuclear pore complex
Recombinant expression: No
SourceSpecies: Homo sapiens (human) / Strain: DLD-1
Source (natural)Organelle: Nuclear envelope / Location in cell: Nuclear envelope

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Experimental details

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Sample preparation

SpecimenSpecimen State: Cell / Method: cryo EM
Sample solutionBuffer solution: PBS / pH: 7.4
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen Name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 2.4 e/Å2 / Illumination Mode: FLOOD BEAM
LensMagnification: 26000.0 X (nominal) / Cs: 2.7 mm / Imaging Mode: BRIGHT FIELD / Defocus: 2500.0 - 5000.0 nm
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: subtomogram averaging / Applied Symmetry: C1 (asymmetric) / Number of Subtomograms: 1252
3D reconstructionResolution: 39 Å / Resolution Method: FSC 0.5 CUT-OFF
FSC plot (resolution estimation)

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