[English] 日本語
Yorodumi- EMDB-5411: The Human Nuclear Pore Complex as Revealed by Cryo-Electron Tomography -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5411 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The Human Nuclear Pore Complex as Revealed by Cryo-Electron Tomography | |||||||||
Map data | Averaged structure of the human nuclear pore complex asymmetric unit | |||||||||
Sample |
| |||||||||
Keywords | Cryo-electron tomography / human nuclear pore complex / nuclear envelope / nucleocytoplasmic transport | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 66.0 Å | |||||||||
Authors | Maimon T / Elad N / Dahan I / Medalia O | |||||||||
Citation | Journal: Structure / Year: 2012 Title: The human nuclear pore complex as revealed by cryo-electron tomography. Authors: Tal Maimon / Nadav Elad / Idit Dahan / Ohad Medalia / Abstract: Nuclear pore complexes (NPCs) are the sole passage through the nuclear envelope, connecting the cytoplasm to the nucleoplasm. These gigantic molecular machines, over 100 MDa in molecular weight, ...Nuclear pore complexes (NPCs) are the sole passage through the nuclear envelope, connecting the cytoplasm to the nucleoplasm. These gigantic molecular machines, over 100 MDa in molecular weight, allow free diffusion of small molecules and ions while mediating selective energy-dependent nucleocytoplasmic transport of large macromolecules. Here, we applied cryo-electron tomography to human fibroblast cells, reconstructing their nuclear envelopes without applying any purification steps. From these reconstructions, we extracted subtomograms containing individual NPCs and utilized in silico subtomogram averaging procedures to determine the structure of the mammalian pore complex at a resolution of ∼6.6 nm. Beyond revealing the canonical features of the human NPC, our analysis identified inner lateral channels and fusing bridge-like structures, suggesting alternative routes of peripheral nuclear passage. Finally, we concluded from our structural analysis that the human NPC is structurally distinct from that of lower eukaryotes in terms of dimension and organization but resembles its amphibian (frog) counterpart. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5411.map.gz | 4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-5411-v30.xml emd-5411.xml | 8.5 KB 8.5 KB | Display Display | EMDB header |
Images | emd_5411.jpg | 47 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5411 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5411 | HTTPS FTP |
-Validation report
Summary document | emd_5411_validation.pdf.gz | 77.6 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_5411_full_validation.pdf.gz | 76.7 KB | Display | |
Data in XML | emd_5411_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5411 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5411 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_5411.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Averaged structure of the human nuclear pore complex asymmetric unit | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 8.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Asymmetric unit of the human nuclear pore complex
Entire | Name: Asymmetric unit of the human nuclear pore complex |
---|---|
Components |
|
-Supramolecule #1000: Asymmetric unit of the human nuclear pore complex
Supramolecule | Name: Asymmetric unit of the human nuclear pore complex / type: sample / ID: 1000 Oligomeric state: octamer (actual refined structure represents an asymmetric unit of the NPC) Number unique components: 1 |
---|
-Supramolecule #1: nuclear pore complex
Supramolecule | Name: nuclear pore complex / type: organelle_or_cellular_component / ID: 1 / Oligomeric state: octamer / Recombinant expression: No / Database: NCBI |
---|---|
Source (natural) | Organism: Homo sapiens (human) / synonym: human / Cell: U2OS / Organelle: Nucleus / Location in cell: Nuclear envelope |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | Details: Dulbecco phosphate buffer saline |
---|---|
Grid | Details: 200 mesh gold grids, silicon coated |
Vitrification | Cryogen name: ETHANE / Instrument: OTHER / Method: Blot for 4 seconds before plunging |
-Electron microscopy
Microscope | FEI POLARA 300 |
---|---|
Temperature | Average: 90 K |
Specialist optics | Energy filter - Name: GIF2002 |
Date | Jan 1, 2010 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 18000 |
Sample stage | Specimen holder: nitrogen cooled / 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
Details | manual selection |
---|---|
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 66.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: TOM_toolbox_software_package / Number subtomograms used: 1696 |