+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31891 | |||||||||
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Title | Structure of Xenopus laevis NPC nuclear ring asymmetric unit | |||||||||
Map data | ||||||||||
Sample |
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Keywords | nuclear pore complex / nuclear ring / asymmetric unit / NUCLEAR PROTEIN | |||||||||
Function / homology | Function and homology information GATOR2 complex / nephron development / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear pore inner ring / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore outer ring / telomere tethering at nuclear periphery / nuclear pore complex assembly / nuclear pore organization ...GATOR2 complex / nephron development / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear pore inner ring / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore outer ring / telomere tethering at nuclear periphery / nuclear pore complex assembly / nuclear pore organization / COPII vesicle coat / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / attachment of mitotic spindle microtubules to kinetochore / structural constituent of nuclear pore / RNA export from nucleus / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / mitotic metaphase chromosome alignment / positive regulation of TOR signaling / cellular response to nutrient levels / mRNA transport / mRNA export from nucleus / nuclear pore / positive regulation of TORC1 signaling / cellular response to amino acid starvation / nuclear periphery / kinetochore / protein import into nucleus / protein transport / nuclear membrane / cell division / lysosomal membrane / structural molecule activity / positive regulation of DNA-templated transcription / DNA binding / RNA binding / nucleoplasm / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Xenopus laevis (African clawed frog) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.1 Å | |||||||||
Authors | Tai L / Zhu Y | |||||||||
Funding support | 1 items
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Citation | Journal: Protein Cell / Year: 2022 Title: 8 Å structure of the outer rings of the Xenopus laevis nuclear pore complex obtained by cryo-EM and AI. Authors: Linhua Tai / Yun Zhu / He Ren / Xiaojun Huang / Chuanmao Zhang / Fei Sun / Abstract: The nuclear pore complex (NPC), one of the largest protein complexes in eukaryotes, serves as a physical gate to regulate nucleocytoplasmic transport. Here, we determined the 8 Å resolution cryo- ...The nuclear pore complex (NPC), one of the largest protein complexes in eukaryotes, serves as a physical gate to regulate nucleocytoplasmic transport. Here, we determined the 8 Å resolution cryo-electron microscopic (cryo-EM) structure of the outer rings containing nuclear ring (NR) and cytoplasmic ring (CR) from the Xenopus laevis NPC, with local resolutions reaching 4.9 Å. With the aid of AlphaFold2, we managed to build a pseudoatomic model of the outer rings, including the Y complexes and flanking components. In this most comprehensive and accurate model of outer rings to date, the almost complete Y complex structure exhibits much tighter interaction in the hub region. In addition to two copies of Y complexes, each asymmetric subunit in CR contains five copies of Nup358, two copies of the Nup214 complex, two copies of Nup205 and one copy of newly identified Nup93, while that in NR contains one copy of Nup205, one copy of ELYS and one copy of Nup93. These in-depth structural features represent a great advance in understanding the assembly of NPCs. | |||||||||
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_31891.map.gz | 117.2 MB | EMDB map data format | |
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Header (meta data) | emd-31891-v30.xml emd-31891.xml | 33.1 KB 33.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_31891_fsc.xml | 11.1 KB | Display | FSC data file |
Images | emd_31891.png | 40.8 KB | ||
Masks | emd_31891_msk_1.map | 125 MB | Mask map | |
Filedesc metadata | emd-31891.cif.gz | 12.7 KB | ||
Others | emd_31891_half_map_1.map.gz emd_31891_half_map_2.map.gz | 115.1 MB 115.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31891 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31891 | HTTPS FTP |
-Validation report
Summary document | emd_31891_validation.pdf.gz | 924.5 KB | Display | EMDB validaton report |
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Full document | emd_31891_full_validation.pdf.gz | 924.1 KB | Display | |
Data in XML | emd_31891_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | emd_31891_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31891 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31891 | HTTPS FTP |
-Related structure data
Related structure data | 7vciMC 7vopC 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_31891.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 2.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_31891_msk_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_31891_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_31891_half_map_2.map | ||||||||||||
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Density Histograms |
-Sample components
+Entire : nuclear pore complex
+Supramolecule #1: nuclear pore complex
+Macromolecule #1: Nuclear pore complex protein Nup85
+Macromolecule #2: MGC154553 protein
+Macromolecule #3: Nucleoporin SEH1-A
+Macromolecule #4: Nup160
+Macromolecule #5: MGC83926 protein
+Macromolecule #6: Nuclear pore complex protein Nup96
+Macromolecule #7: GATOR complex protein SEC13
+Macromolecule #8: Nuclear pore complex protein
+Macromolecule #9: outer Nup133
+Macromolecule #10: MGC83295 protein
+Macromolecule #11: Protein ELYS
+Macromolecule #12: Nuclear pore complex protein Nup93
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |