+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0998 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Nuclear ring of the Xenopus laevis nuclear pore complex | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Biological species | Xenopus laevis (African clawed frog) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 13.6 Å | |||||||||
Authors | Li S / Zhang YQ | |||||||||
Citation | Journal: Cell Res / Year: 2020 Title: Molecular architecture of the luminal ring of the Xenopus laevis nuclear pore complex. Authors: Yanqing Zhang / Sai Li / Chao Zeng / Gaoxingyu Huang / Xuechen Zhu / Qifan Wang / Kunpeng Wang / Qiang Zhou / Chuangye Yan / Wusheng Zhang / Guangwen Yang / Minhao Liu / Qinghua Tao / Jianlin Lei / Yigong Shi / Abstract: The nuclear pore complex (NPC) mediates the flow of substances between the nucleus and cytoplasm in eukaryotic cells. Here we report the cryo-electron tomography (cryo-ET) structure of the luminal ...The nuclear pore complex (NPC) mediates the flow of substances between the nucleus and cytoplasm in eukaryotic cells. Here we report the cryo-electron tomography (cryo-ET) structure of the luminal ring (LR) of the NPC from Xenopus laevis oocyte. The observed key structural features of the LR are independently confirmed by single-particle cryo-electron microscopy (cryo-EM) analysis. The LR comprises eight butterfly-shaped subunits, each containing two symmetric wings. Each wing consists of four elongated, tubular protomers. Within the LR subunit, the eight protomers form a Finger domain, which directly contacts the fusion between the inner and outer nuclear membranes and a Grid domain, which serves as a rigid base for the Finger domain. Two neighboring LR subunits interact with each other through the lateral edges of their wings to constitute a Bumper domain, which displays two major conformations and appears to cushion neighboring NPCs. Our study reveals previously unknown features of the LR and potentially explains the elastic property of the NPC. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0998.map.gz | 2.2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-0998-v30.xml emd-0998.xml | 12.3 KB 12.3 KB | Display Display | EMDB header |
Images | emd_0998.png | 41.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0998 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0998 | HTTPS FTP |
-Validation report
Summary document | emd_0998_validation.pdf.gz | 79.4 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_0998_full_validation.pdf.gz | 78.5 KB | Display | |
Data in XML | emd_0998_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0998 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0998 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_0998.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 4.444 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Xenopus Laevis
Entire | Name: Xenopus Laevis (African clawed frog) |
---|---|
Components |
|
-Supramolecule #1: Xenopus Laevis
Supramolecule | Name: Xenopus Laevis / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Xenopus laevis (African clawed frog) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.5 / Component - Concentration: 1.6 M / Component - Formula: NaCl / Component - Name: sodium chloride |
---|---|
Grid | Model: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-8 / Average exposure time: 0.8 sec. / Average electron dose: 2.93 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 4.0 µm / Calibrated defocus min: 2.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 64000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |