+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0909 | |||||||||
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Title | core region reconstruction. | |||||||||
Map data | core region reconstruction | |||||||||
Sample |
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Function / homology | Function and homology information macromolecule localization / nitrogen compound transport / GATOR2 complex / nephron development / organic substance transport / macromolecule metabolic process / nuclear pore organization / nuclear pore outer ring / attachment of mitotic spindle microtubules to kinetochore / structural constituent of nuclear pore ...macromolecule localization / nitrogen compound transport / GATOR2 complex / nephron development / organic substance transport / macromolecule metabolic process / nuclear pore organization / nuclear pore outer ring / attachment of mitotic spindle microtubules to kinetochore / structural constituent of nuclear pore / nucleocytoplasmic transport / mitotic metaphase chromosome alignment / cellular response to nutrient levels / intracellular transport / mRNA transport / nuclear pore / positive regulation of TORC1 signaling / kinetochore / protein transport / nuclear membrane / lysosomal membrane / cell division / structural molecule activity / metal ion binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Xenopus laevis (African clawed frog) / African clawed frog (African clawed frog) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.5 Å | |||||||||
Authors | Shi Y / Huang G / Yan C / Zhang Y | |||||||||
Funding support | China, 2 items
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Citation | Journal: Cell Res / Year: 2020 Title: Structure of the cytoplasmic ring of the Xenopus laevis nuclear pore complex by cryo-electron microscopy single particle analysis. Authors: Gaoxingyu Huang / Yanqing Zhang / Xuechen Zhu / Chao Zeng / Qifan Wang / Qiang Zhou / Qinghua Tao / Minhao Liu / Jianlin Lei / Chuangye Yan / Yigong Shi / Abstract: The nuclear pore complex (NPC) exhibits structural plasticity and has only been characterized at local resolutions of up to 15 Å for the cytoplasmic ring (CR). Here we present a single-particle ...The nuclear pore complex (NPC) exhibits structural plasticity and has only been characterized at local resolutions of up to 15 Å for the cytoplasmic ring (CR). Here we present a single-particle cryo-electron microscopy (cryo-EM) structure of the CR from Xenopus laevis NPC at average resolutions of 5.5-7.9 Å, with local resolutions reaching 4.5 Å. Improved resolutions allow identification and placement of secondary structural elements in the majority of the CR components. The two Y complexes in each CR subunit interact with each other and associate with those from flanking subunits, forming a circular scaffold. Within each CR subunit, the Nup358-containing region wraps around the stems of both Y complexes, likely stabilizing the scaffold. Nup205 connects the short arms of the two Y complexes and associates with the stem of a neighboring Y complex. The Nup214-containing region uses an extended coiled-coil to link Nup85 of the two Y complexes and protrudes into the axial pore of the NPC. These previously uncharacterized structural features reveal insights into NPC assembly. | |||||||||
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_0909.map.gz | 58.9 MB | EMDB map data format | |
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Header (meta data) | emd-0909-v30.xml emd-0909.xml | 37.3 KB 37.3 KB | Display Display | EMDB header |
Images | emd_0909.png | 46 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0909 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0909 | HTTPS FTP |
-Related structure data
Related structure data | 6lk8MC 0910C 0911C 0982C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0909.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | core region reconstruction | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.222 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 : Cytoplasmic Ring Subunit of Xenopus laevis NPC
+Supramolecule #1: Cytoplasmic Ring Subunit of Xenopus laevis NPC
+Macromolecule #1: MGC83295 protein
+Macromolecule #2: Nuclear pore complex protein Nup85
+Macromolecule #3: MGC154553 protein
+Macromolecule #4: Nucleoporin SEH1-A
+Macromolecule #5: outer Nup160
+Macromolecule #6: MGC83926 protein
+Macromolecule #7: Nuclear pore complex protein Nup96
+Macromolecule #8: GATOR complex protein SEC13
+Macromolecule #9: Nuclear pore complex protein
+Macromolecule #10: outer Nup133
+Macromolecule #11: Nup358 complex, clamps
+Macromolecule #12: Nup214 complex Coiled-coil region 1, helix 1
+Macromolecule #13: Nup214 complex coiled coil region 1, helix 2
+Macromolecule #14: Nup214 complex coiled coil region 1, helix 3
+Macromolecule #15: Nup214 complex Coiled coil region 2, helix 1
+Macromolecule #16: Nup214 complex Coiled coil region 2, helix 2
+Macromolecule #17: Nup214 complex Coiled coil region 2, helix 3
+Macromolecule #18: bridge domain
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | tissue |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil / Material: COPPER |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 75.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 616547 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-6lk8: |