+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2443 | |||||||||
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Title | Electron microscopy of the human Nup107 subcomplex | |||||||||
Map data | Reconstruction of the human Nup107 subcomplex | |||||||||
Sample |
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Keywords | nuclear pore complex / Nup107 subcomplex / scaffold nucleoporins | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | subtomogram averaging / Resolution: 34.0 Å | |||||||||
Authors | Bui KH / von Appen A / DiGuilio AL / Ori A / Sparks L / Mackmull MT / Bock T / Hagen W / Andres-Pons A / Glavy JS / Beck M | |||||||||
Citation | Journal: Cell / Year: 2013 Title: Integrated structural analysis of the human nuclear pore complex scaffold. Authors: Khanh Huy Bui / Alexander von Appen / Amanda L DiGuilio / Alessandro Ori / Lenore Sparks / Marie-Therese Mackmull / Thomas Bock / Wim Hagen / Amparo Andrés-Pons / Joseph S Glavy / Martin Beck / Abstract: The nuclear pore complex (NPC) is a fundamental component of all eukaryotic cells that facilitates nucleocytoplasmic exchange of macromolecules. It is assembled from multiple copies of about 30 ...The nuclear pore complex (NPC) is a fundamental component of all eukaryotic cells that facilitates nucleocytoplasmic exchange of macromolecules. It is assembled from multiple copies of about 30 nucleoporins. Due to its size and complex composition, determining the structure of the NPC is an enormous challenge, and the overall architecture of the NPC scaffold remains elusive. In this study, we have used an integrated approach based on electron tomography, single-particle electron microscopy, and crosslinking mass spectrometry to determine the structure of a major scaffold motif of the human NPC, the Nup107 subcomplex, in both isolation and integrated into the NPC. We show that 32 copies of the Nup107 subcomplex assemble into two reticulated rings, one each at the cytoplasmic and nuclear face of the NPC. This arrangement may explain how changes of the diameter are realized that would accommodate transport of huge cargoes. | |||||||||
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_2443.map.gz | 2.1 MB | EMDB map data format | |
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Header (meta data) | emd-2443-v30.xml emd-2443.xml | 9.8 KB 9.8 KB | Display Display | EMDB header |
Images | emd_2443.png | 55.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2443 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2443 | HTTPS FTP |
-Validation report
Summary document | emd_2443_validation.pdf.gz | 204.9 KB | Display | EMDB validaton report |
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Full document | emd_2443_full_validation.pdf.gz | 204 KB | Display | |
Data in XML | emd_2443_validation.xml.gz | 5.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2443 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2443 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2443.map.gz / Format: CCP4 / Size: 2.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of the human Nup107 subcomplex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 5.84 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 : human Nup107 subcomplex
Entire | Name: human Nup107 subcomplex |
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Components |
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-Supramolecule #1000: human Nup107 subcomplex
Supramolecule | Name: human Nup107 subcomplex / type: sample / ID: 1000 Details: The sample was affinity purified from HEK cells arrested by nocodazole. Number unique components: 1 |
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Molecular weight | Method: Gel filtration |
-Macromolecule #1: Human Nup107 subcomplex
Macromolecule | Name: Human Nup107 subcomplex / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Organelle: Nucleus / Location in cell: Nuclear pore complex |
-Experimental details
-Structure determination
Processing | subtomogram averaging |
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Aggregation state | particle |
-Sample preparation
Grid | Details: 300 mesh Quantifoil Continous Carbon Support Copper Grid |
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Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Nov 26, 2010 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 300 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 51369 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 34000 |
Sample stage | Specimen holder: Gatan 626, liquid nitrogen cooled / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 ° |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | We used a hybrid approach in which the primary data were acquired using a tomographic acquisition scheme, subtomograms were projected for two-dimensional classification and the resulting classes subjected to subtomogram averaging. |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 34.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMOD, SPIDER, TOM, AV3 / Number subtomograms used: 205 |
CTF correction | Details: CTF phase flip of each tomogram |