[English] 日本語
Yorodumi- EMDB-11375: In cellulo nuclear pore complex in constricted conformation from ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11375 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | In cellulo nuclear pore complex in constricted conformation from energy depleted S. pombe cells | |||||||||
Map data | In cellulo nuclear pore complex with constricted diameter from energy depleted S. pombe cells | |||||||||
Sample |
| |||||||||
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 / 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 / Transport of Mature mRNA derived from an Intron-Containing Transcript / 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 / 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 / Transport of Mature mRNA derived from an Intron-Containing Transcript / Transcriptional regulation by small RNAs / GATOR2 complex / Seh1-associated complex / nuclear pore inner ring / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear pore outer ring / nuclear pore organization / COPII vesicle coat / structural constituent of nuclear pore / RNA export from nucleus / nucleocytoplasmic transport / vacuolar membrane / 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 / protein export from nucleus / positive regulation of TORC1 signaling / cellular response to amino acid starvation / nuclear periphery / protein import into nucleus / protein transport / nuclear envelope / endoplasmic reticulum membrane / structural molecule activity / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 28.0 Å | |||||||||
Authors | Zimmerli CE / Allegretti M / Rantos V / Goetz S / Obarska-Kosinska A / Zagoriy I / Hummer G / Mahamid J / Kosinski J / Beck M | |||||||||
Citation | Journal: 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11375.map.gz | 9.1 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-11375-v30.xml emd-11375.xml | 8.8 KB 8.8 KB | Display Display | EMDB header |
Images | emd_11375.png | 38.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11375 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11375 | HTTPS FTP |
-Validation report
Summary document | emd_11375_validation.pdf.gz | 314.7 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_11375_full_validation.pdf.gz | 314.2 KB | Display | |
Data in XML | emd_11375_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | emd_11375_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11375 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11375 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_11375.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | In cellulo nuclear pore complex with constricted diameter from energy depleted S. pombe cells | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 6.9 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : energy depleted S. pombe cells
Entire | Name: energy depleted S. pombe cells |
---|---|
Components |
|
-Supramolecule #1: energy depleted S. pombe cells
Supramolecule | Name: energy depleted S. pombe cells / type: complex / ID: 1 / Parent: 0 |
---|---|
Source (natural) | Organism: Schizosaccharomyces pombe (fission yeast) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 6.5 |
---|---|
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Average electron dose: 3.9 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C8 (8 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 533 |
---|---|
Extraction | Number tomograms: 76 / Number images used: 292 |
Final angle assignment | Type: OTHER |