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- EMDB-13081: In cellulo nuclear pore complex from S. pombe cells exposed to a ... -

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Basic information

Entry
Database: EMDB / ID: EMD-13081
TitleIn cellulo nuclear pore complex from S. pombe cells exposed to a hypertonic osmotic shock
Map dataMap of the in cellulo S. pombe NPC from cells exposed to hyperosmotic shock
Sample
  • Complex: In cellulo nuclear pore complex from S. pombe cells
Function / homology
Function and homology information


COPII-mediated vesicle transport / Transport of the SLBP independent Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of chromatin organization proteins / Transcriptional regulation by small RNAs ...COPII-mediated vesicle transport / Transport of the SLBP independent Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of chromatin organization proteins / Transcriptional regulation by small RNAs / GATOR2 complex / Seh1-associated complex / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear pore inner ring / nuclear pore outer ring / nuclear pore organization / COPII vesicle coat / structural constituent of nuclear pore / NLS-bearing protein import into nucleus / RNA export from nucleus / vacuolar membrane / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / positive regulation of TOR signaling / mRNA transport / nuclear pore / mRNA export from nucleus / protein export from nucleus / positive regulation of TORC1 signaling / nuclear periphery / cellular response to amino acid starvation / protein import into nucleus / protein transport / nuclear envelope / endoplasmic reticulum membrane / structural molecule activity / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Nucleoporin NUP120, helical domain / Nuclear pore protein Nup188, C-terminal / Nuclear pore protein NUP188 C-terminal domain / Nucleoporin Nup120/160, beta-propeller domain / Nucleoporin Nup37 / Nucleoporin Nup188 / : / Nucleoporin Nup188, N-terminal subdomain III / Nucleoporin Nup120/160 ...: / Nucleoporin NUP120, helical domain / Nuclear pore protein Nup188, C-terminal / Nuclear pore protein NUP188 C-terminal domain / Nucleoporin Nup120/160, beta-propeller domain / Nucleoporin Nup37 / Nucleoporin Nup188 / : / Nucleoporin Nup188, N-terminal subdomain III / Nucleoporin Nup120/160 / Nucleoporin Nup186/Nup192/Nup205 / Nuclear pore complex scaffold, nucleoporins 186/192/205 / Sec13/Seh1 family / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / 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: 25.0 Å
AuthorsZimmerli CE / Allegretti M / Rantos V / Goetz S / Obarska-Kosinska A / Zagoriy I / 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
DepositionJun 14, 2021-
Header (metadata) releaseJul 28, 2021-
Map releaseJul 28, 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: 0.095
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.095
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13081.png

Downloads & links

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Map

FileDownload / File: emd_13081.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of the in cellulo S. pombe NPC from cells exposed to hyperosmotic shock
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.74 Å/pix.
x 288 pix.
= 1941.12 Å		6.74 Å/pix.
x 288 pix.
= 1941.12 Å		6.74 Å/pix.
x 288 pix.
= 1941.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.095 / Movie #1: 0.095
Minimum - Maximum-0.25439644 - 0.54331505
Average (Standard dev.)0.019120088 (±0.02486423)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 1941.1199 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.746.746.74
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z1941.1201941.1201941.120
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.2540.5430.019

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Supplemental data

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Sample components

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Entire : In cellulo nuclear pore complex from S. pombe cells

EntireName: In cellulo nuclear pore complex from S. pombe cells
Components
  • Complex: In cellulo nuclear pore complex from S. pombe cells

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Supramolecule #1: In cellulo nuclear pore complex from S. pombe cells

SupramoleculeName: In cellulo nuclear pore complex from 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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 3.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 42000
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: 25.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 1063
ExtractionNumber tomograms: 57 / Number images used: 200 / Software - Name: NOVACTF
Final angle assignmentType: OTHER

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