+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3008 | |||||||||
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Title | Nuclear envelope of the native X. laevis nuclear pore complex. | |||||||||
Map data | Recommended UCSF Chimera hide dust setting: size 1400.0 | |||||||||
Sample |
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Keywords | X. laevis / Nuclear pore complex / Nuclear envelope | |||||||||
Biological species | Xenopus laevis (African clawed frog) | |||||||||
Method | subtomogram averaging / cryo EM | |||||||||
Authors | Eibauer M / Pellanda M / Turgay Y / Dubrovsky A / Wild A / Medalia O | |||||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Structure and gating of the nuclear pore complex. Authors: Matthias Eibauer / Mauro Pellanda / Yagmur Turgay / Anna Dubrovsky / Annik Wild / Ohad Medalia / Abstract: Nuclear pore complexes (NPCs) perforate the nuclear envelope and allow the exchange of macromolecules between the nucleus and the cytoplasm. To acquire a deeper understanding of this transport ...Nuclear pore complexes (NPCs) perforate the nuclear envelope and allow the exchange of macromolecules between the nucleus and the cytoplasm. To acquire a deeper understanding of this transport mechanism, we analyse the structure of the NPC scaffold and permeability barrier, by reconstructing the Xenopus laevis oocyte NPC from native nuclear envelopes up to 20 Å resolution by cryo-electron tomography in conjunction with subtomogram averaging. In addition to resolving individual protein domains of the NPC constituents, we propose a model for the architecture of the molecular gate at its central channel. Furthermore, we compare and contrast this native NPC structure to one that exhibits reduced transport activity and unveil the spatial properties of the NPC gate. | |||||||||
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_3008.map.gz | 2.3 MB | EMDB map data format | |
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Header (meta data) | emd-3008-v30.xml emd-3008.xml | 9.4 KB 9.4 KB | Display Display | EMDB header |
Images | emd_3008.tif | 1.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3008 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3008 | HTTPS FTP |
-Validation report
Summary document | emd_3008_validation.pdf.gz | 213.9 KB | Display | EMDB validaton report |
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Full document | emd_3008_full_validation.pdf.gz | 213.1 KB | Display | |
Data in XML | emd_3008_validation.xml.gz | 6.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3008 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3008 | HTTPS FTP |
-Related structure data
Related structure data | 3005C 3006C 3007C 3009C 3010C 3011C 3012C C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3008.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Recommended UCSF Chimera hide dust setting: size 1400.0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 6.6 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 : X. laevis nuclear pore complex
Entire | Name: X. laevis nuclear pore complex |
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Components |
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-Supramolecule #1000: X. laevis nuclear pore complex
Supramolecule | Name: X. laevis nuclear pore complex / type: sample / ID: 1000 Details: The sample is spreaded X. laevis nuclear envelope containing nuclear pore complexes Number unique components: 1 |
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-Macromolecule #1: Nuclear pore complex
Macromolecule | Name: Nuclear pore complex / type: protein_or_peptide / ID: 1 / Name.synonym: NPC / Recombinant expression: No |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) / synonym: African clawed frog / Cell: Oocyte / Organelle: Nucleus / Location in cell: Nuclear envelope |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER |
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-Electron microscopy
Microscope | FEI POLARA 300 |
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Specialist optics | Energy filter - Name: GIF Quantum / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Date | Jun 10, 2013 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 20 e/Å2 |
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: 6.5 µm / Nominal defocus min: 5.5 µm |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 ° |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Software - Name: TOM / Details: Protomer averaging, subprotomer averaging / Number subtomograms used: 5478 |
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CTF correction | Details: Whole micrograph |