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- EMDB-11374: In cellulo nuclear pore complex with intermediate diameter from e... -

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Basic information

Entry
Database: EMDB / ID: EMD-11374
TitleIn cellulo nuclear pore complex with intermediate diameter from energy depleted S. pombe cells
Map dataIn cellulo nuclear pore complex with intermediate diameter from energy depelted S. pombe cells
Sample
  • Complex: energy depleted S. pombe cells
Function / homology
Function and homology information


COPII-mediated vesicle transport / Regulation of HSF1-mediated heat shock response / Transport of the SLBP independent Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / Postmitotic nuclear pore complex (NPC) reformation / Transcriptional regulation by small RNAs / SUMOylation of chromatin organization proteins / Transport of Mature mRNA derived from an Intron-Containing Transcript ...COPII-mediated vesicle transport / Regulation of HSF1-mediated heat shock response / Transport of the SLBP independent Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / Postmitotic nuclear pore complex (NPC) reformation / Transcriptional regulation by small RNAs / SUMOylation of chromatin organization proteins / Transport of Mature mRNA derived from an Intron-Containing Transcript / GATOR2 complex / nuclear pore inner ring / Seh1-associated complex / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear pore organization / nuclear pore outer ring / COPII vesicle coat / TORC1 signaling / structural constituent of nuclear pore / RNA export from nucleus / vacuolar membrane / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / NLS-bearing protein import into nucleus / positive regulation of TOR signaling / mRNA transport / mRNA export from nucleus / nuclear pore / positive regulation of TORC1 signaling / cellular response to amino acid starvation / protein export from nucleus / nuclear periphery / protein import into nucleus / protein transport / nuclear envelope / endoplasmic reticulum membrane / structural molecule activity / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Nucleoporin NUP120, helical domain / Nucleoporin Nup120/160 / Nuclear pore protein Nup188, C-terminal / Nuclear pore protein NUP188 C-terminal domain / : / Nucleoporin Nup188, N-terminal subdomain III / Nucleoporin Nup37 / Nucleoporin Nup188 / Nucleoporin Nup120/160 ...: / Nucleoporin NUP120, helical domain / Nucleoporin Nup120/160 / Nuclear pore protein Nup188, C-terminal / Nuclear pore protein NUP188 C-terminal domain / : / Nucleoporin Nup188, N-terminal subdomain III / Nucleoporin Nup37 / Nucleoporin Nup188 / Nucleoporin Nup120/160 / Nucleoporin Nup186/Nup192/Nup205 / Nuclear pore complex scaffold, nucleoporins 186/192/205 / Sec13/Seh1 family / 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
Uncharacterized WD repeat-containing protein C4F10.18 / Nucleoporin nup120 / Protein transport protein sec13 / Nucleoporin nup186 / Nucleoporin seh1 / Nucleoporin nup184
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 27.0 Å
AuthorsZimmerli CE / Allegretti M / Rantos V / Goetz S / Obarska-Kosinska A / Zagoriy I / Hummer G / Mahamid J / Kosinski J / Beck M
CitationJournal: Science / Year: 2021
Title: Nuclear pores dilate and constrict in cellulo.
Authors: Christian E Zimmerli / Matteo Allegretti / Vasileios Rantos / Sara K Goetz / Agnieszka Obarska-Kosinska / Ievgeniia Zagoriy / Aliaksandr Halavatyi / Gerhard Hummer / Julia Mahamid / Jan Kosinski / Martin Beck /
Abstract: In eukaryotic cells, nuclear pore complexes (NPCs) fuse the inner and outer nuclear membranes and mediate nucleocytoplasmic exchange. They are made of 30 different nucleoporins and form a cylindrical ...In eukaryotic cells, nuclear pore complexes (NPCs) fuse the inner and outer nuclear membranes and mediate nucleocytoplasmic exchange. They are made of 30 different nucleoporins and form a cylindrical architecture around an aqueous central channel. This architecture is highly dynamic in space and time. Variations in NPC diameter have been reported, but the physiological circumstances and the molecular details remain unknown. Here, we combined cryo–electron tomography with integrative structural modeling to capture a molecular movie of the respective large-scale conformational changes in cellulo. Although NPCs of exponentially growing cells adopted a dilated conformation, they reversibly constricted upon cellular energy depletion or conditions of hypertonic osmotic stress. Our data point to a model where the nuclear envelope membrane tension is linked to the conformation of the NPC.
History
DepositionJul 10, 2020-
Header (metadata) releaseJul 21, 2021-
Map releaseJul 21, 2021-
UpdateFeb 9, 2022-
Current statusFeb 9, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.821
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.821
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11374.png

Downloads & links

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Map

FileDownload / File: emd_11374.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIn cellulo nuclear pore complex with intermediate diameter from energy depelted S. pombe cells
Voxel sizeX=Y=Z: 6.9 Å
Density
Contour LevelBy AUTHOR: 0.821 / Movie #1: 0.821
Minimum - Maximum-1.2974322 - 2.6029606
Average (Standard dev.)0.33801 (±0.12703243)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 1987.2001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.96.96.9
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z1987.2001987.2001987.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-1.2972.6030.338

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Supplemental data

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Sample components

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Entire : energy depleted S. pombe cells

EntireName: energy depleted S. pombe cells
Components
  • Complex: energy depleted S. pombe cells

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Supramolecule #1: energy depleted S. pombe cells

SupramoleculeName: energy depleted S. pombe cells / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)

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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: 6.5
VitrificationCryogen name: ETHANE-PROPANE

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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 / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Average electron dose: 3.9 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 76 / Number images used: 292
Final angle assignmentType: OTHER
Final reconstructionApplied symmetry - Point group: C8 (8 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 27.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 1012

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