[English] 日本語
Yorodumi- PDB-7vop: Cryo-EM structure of Xenopus laevis nuclear pore complex cytoplas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vop | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of Xenopus laevis nuclear pore complex cytoplasmic ring subunit | ||||||
Components |
| ||||||
Keywords | NUCLEAR PROTEIN / cytoplasmic ring / cryo-EM / nuclear pore complex / Xenopus laevis | ||||||
Function / homology | Function and homology information macromolecule localization / GATOR2 complex / nephron development / nuclear pore outer ring / nuclear pore complex assembly / nuclear pore organization / telomere tethering at nuclear periphery / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / attachment of mitotic spindle microtubules to kinetochore ...macromolecule localization / GATOR2 complex / nephron development / nuclear pore outer ring / nuclear pore complex assembly / nuclear pore organization / telomere tethering at nuclear periphery / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / attachment of mitotic spindle microtubules to kinetochore / intracellular transport / structural constituent of nuclear pore / RNA export from nucleus / nucleocytoplasmic transport / mitotic metaphase chromosome alignment / nuclear localization sequence binding / ribosomal large subunit export from nucleus / mRNA transport / cellular response to nutrient levels / mRNA export from nucleus / nuclear pore / ribosomal small subunit export from nucleus / positive regulation of TORC1 signaling / nuclear periphery / kinetochore / protein import into nucleus / protein transport / nuclear membrane / lysosomal membrane / cell division / structural molecule activity / RNA binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Xenopus laevis (African clawed frog) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.7 Å | ||||||
Authors | Tai, L. / Zhu, Y. / Sun, F. | ||||||
Funding support | 1items
| ||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7vop.cif.gz | 4 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7vop.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7vop.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vop_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7vop_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 7vop_validation.xml.gz | 519.5 KB | Display | |
Data in CIF | 7vop_validation.cif.gz | 793 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vo/7vop ftp://data.pdbj.org/pub/pdb/validation_reports/vo/7vop | HTTPS FTP |
-Related structure data
Related structure data | 32056MC 7vciC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Nuclear pore complex protein ... , 3 types, 5 molecules AJFOU
#1: Protein | Mass: 75160.047 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q68FJ0 #6: Protein | Mass: 104742.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A0A1B8XZT4 #11: Protein | | Mass: 93565.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q7ZX96 |
---|
-Protein , 12 types, 27 molecules BKCLDMENGPHQIRSTVWXYZaebdcf
#2: Protein | Mass: 41744.512 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q05AW3 #3: Protein | Mass: 39777.566 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q4FZW5 #4: Protein | Mass: 160427.547 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A0A6I8QA34 #5: Protein | Mass: 36588.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q66IZ6 #7: Protein | Mass: 35315.285 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q7ZYJ8 #8: Protein | Mass: 105398.547 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A2RV69 #9: Protein | Mass: 127551.250 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A0A1L8H1I9 #10: Protein | Mass: 227854.141 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q642R6 #12: Protein | Mass: 325736.625 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A0A1L8HGL2 #13: Protein | Mass: 209080.406 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q9PVZ2 #14: Protein | Mass: 82573.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q4KLQ6 #15: Protein | Mass: 55969.496 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q91349 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: nuclear pore complex cytoplasmic ring / Type: COMPLEX / Entity ID: all / Source: NATURAL |
---|---|
Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
---|---|
3D reconstruction | Resolution: 8.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 354460 / Symmetry type: POINT |