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Yorodumi- EMDB-1394: Snapshots of nuclear pore complexes in action captured by cryo-el... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1394 | |||||||||
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Title | Snapshots of nuclear pore complexes in action captured by cryo-electron tomography. | |||||||||
Map data | asymmetric unit of Dictyostelium discoideum nuclear pore complex | |||||||||
Sample |
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Biological species | Dictyostelium discoideum (eukaryote) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 58.0 Å | |||||||||
Authors | Beck M / Lucic V / Forster F / Baumeister W / Medalia O | |||||||||
Citation | Journal: Nature / Year: 2007 Title: Snapshots of nuclear pore complexes in action captured by cryo-electron tomography. Authors: Martin Beck / Vladan Lucić / Friedrich Förster / Wolfgang Baumeister / Ohad Medalia / Abstract: Nuclear pore complexes reside in the nuclear envelope of eukaryotic cells and mediate the nucleocytoplasmic exchange of macromolecules. Traffic is regulated by mobile transport receptors that target ...Nuclear pore complexes reside in the nuclear envelope of eukaryotic cells and mediate the nucleocytoplasmic exchange of macromolecules. Traffic is regulated by mobile transport receptors that target their cargo to the central translocation channel, where phenylalanine-glycine-rich repeats serve as binding sites. The structural analysis of the nuclear pore is a formidable challenge given its size, its location in a membranous environment and its dynamic nature. Here we have used cryo-electron tomography to study the structure of nuclear pore complexes in their functional environment, that is, in intact nuclei of Dictyostelium discoideum. A new image-processing strategy compensating for deviations of the asymmetric units (protomers) from a perfect eight-fold symmetry enabled us to refine the structure and to identify new features. Furthermore, the superposition of a large number of tomograms taken in the presence of cargo, which was rendered visible by gold nanoparticles, has yielded a map outlining the trajectories of import cargo. Finally, we have performed single-molecule Monte Carlo simulations of nuclear import to interpret the experimentally observed cargo distribution in the light of existing models for nuclear import. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1394.map.gz | 684.4 KB | EMDB map data format | |
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Header (meta data) | emd-1394-v30.xml emd-1394.xml | 8.7 KB 8.7 KB | Display Display | EMDB header |
Images | EMD-1394.png | 273.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1394 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1394 | HTTPS FTP |
-Validation report
Summary document | emd_1394_validation.pdf.gz | 208 KB | Display | EMDB validaton report |
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Full document | emd_1394_full_validation.pdf.gz | 207.2 KB | Display | |
Data in XML | emd_1394_validation.xml.gz | 5.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1394 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1394 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_1394.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | asymmetric unit of Dictyostelium discoideum nuclear pore complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 16.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : nuclear pore complex
Entire | Name: nuclear pore complex |
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Components |
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-Supramolecule #1000: nuclear pore complex
Supramolecule | Name: nuclear pore complex / type: sample / ID: 1000 Oligomeric state: octamer (actual refined structure represents an asymmetric unit of the NPC) Number unique components: 1 |
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-Supramolecule #1: nuclear pore
Supramolecule | Name: nuclear pore / type: organelle_or_cellular_component / ID: 1 / Name.synonym: nuclear pore / Oligomeric state: octamer / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Dictyostelium discoideum (eukaryote) / Strain: AX2 / Organelle: Nucleus / Location in cell: nuclear enveope |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 Details: 50 mM Tris pH 7.6, 25 mM KCl, 5mM MgCl2, 50 mM sucrose |
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Grid | Details: 200 mesh copper grid |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Rudolf Gatz plunger |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Temperature | Average: 90 K |
Specialist optics | Energy filter - Name: GIF2002 / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Image recording | Category: CCD / Film or detector model: GENERIC CCD |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 27500 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: OTHER / Tilt series - Axis1 - Min angle: -63 ° / Tilt series - Axis1 - Max angle: 63 ° |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
Details | Average number of projections used in the 3D reconstructions: 4184. |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 58.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: TOM |