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- PDB-7vci: Structure of Xenopus laevis NPC nuclear ring asymmetric unit -

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Basic information

Entry
Database: PDB / ID: 7vci
TitleStructure of Xenopus laevis NPC nuclear ring asymmetric unit
Components
  • (Nuclear pore complex protein ...) x 3
  • GATOR complex protein SEC13
  • MGC154553 protein
  • MGC83295 protein
  • MGC83926 protein
  • Nuclear pore complex protein
  • Nucleoporin SEH1-A
  • Nup160
  • Protein ELYS
  • outer Nup133
KeywordsNUCLEAR PROTEIN / nuclear pore complex / nuclear ring / asymmetric unit
Function / homology
Function and homology information


system development / nephron development / GATOR2 complex / Seh1-associated complex / nuclear pore inner ring / animal organ development / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore complex assembly ...system development / nephron development / GATOR2 complex / Seh1-associated complex / nuclear pore inner ring / animal organ development / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore complex assembly / nuclear pore outer ring / nuclear pore organization / COPII vesicle coat / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / attachment of mitotic spindle microtubules to kinetochore / structural constituent of nuclear pore / poly(A)+ mRNA export from nucleus / mitotic metaphase chromosome alignment / positive regulation of TOR signaling / mRNA transport / nuclear pore / mRNA export from nucleus / cellular response to nutrient levels / serine-type peptidase activity / positive regulation of TORC1 signaling / nuclear periphery / cellular response to amino acid starvation / chromosome segregation / kinetochore / protein import into nucleus / protein transport / nuclear membrane / lysosomal membrane / cell division / positive regulation of DNA-templated transcription / structural molecule activity / proteolysis / DNA binding / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
ELYS, beta-propeller domain / : / beta-propeller of ELYS nucleoporin / ELYS-like domain / Nuclear pore complex assembly / Nucleoporin Nup37 / Nup98, Gle2-binding sequence / Nucleoporin Nup85-like / Nup85 Nucleoporin / Nuclear pore protein 84/107 ...ELYS, beta-propeller domain / : / beta-propeller of ELYS nucleoporin / ELYS-like domain / Nuclear pore complex assembly / Nucleoporin Nup37 / Nup98, Gle2-binding sequence / Nucleoporin Nup85-like / Nup85 Nucleoporin / Nuclear pore protein 84/107 / Nuclear pore protein 84 / 107 / Nuclear pore complex protein Nup133-like / Nucleoporin Nup186/Nup192/Nup205 / Nuclear pore complex scaffold, nucleoporins 186/192/205 / Nucleoporin interacting component Nup93/Nic96 / Nup93/Nic96 / Nucleoporin FG repeat / Nucleoporin FG repeat region / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Sec13/Seh1 family / Nucleoporin peptidase S59-like / Nup98-96 autopeptidase S59 / NUP C-terminal domain profile. / Quinoprotein alcohol dehydrogenase-like superfamily / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Nuclear pore complex protein Nup98-Nup96 / Nuclear pore complex protein Nup133 / Nuclear pore complex protein / MGC154553 protein / Nucleoporin SEH1-A / Protein ELYS / MGC83295 protein / Nucleoporin Nup37 / Nuclear pore complex protein Nup85 / Nuclear pore complex protein Nup93 / Protein SEC13 homolog
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.1 Å
AuthorsTai, L. / Zhu, Y. / Sun, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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
DepositionSep 3, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Assembly

Deposited unit
A: Nuclear pore complex protein Nup85
B: MGC154553 protein
C: Nucleoporin SEH1-A
D: Nup160
E: MGC83926 protein
F: Nuclear pore complex protein Nup96
G: GATOR complex protein SEC13
H: Nuclear pore complex protein
I: outer Nup133
J: Nuclear pore complex protein Nup85
K: MGC154553 protein
L: Nucleoporin SEH1-A
M: Nup160
N: MGC83926 protein
O: Nuclear pore complex protein Nup96
P: GATOR complex protein SEC13
Q: Nuclear pore complex protein
R: outer Nup133
S: MGC83295 protein
T: Protein ELYS
U: Nuclear pore complex protein Nup93


Theoretical massNumber of molelcules
Total (without water)2,048,95521
Polymers2,048,95521
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Nuclear pore complex protein ... , 3 types, 5 molecules AJFOU

#1: Protein Nuclear pore complex protein Nup85 / 85 kDa nucleoporin / Nucleoporin Nup85


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 Nuclear pore complex protein Nup96 / Nuclear pore complex protein Nup98 / Nuclear pore complex protein Nup98-Nup96 / Nucleoporin Nup96 / ...Nuclear pore complex protein Nup98 / Nuclear pore complex protein Nup98-Nup96 / Nucleoporin Nup96 / Nucleoporin Nup98


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
#12: Protein Nuclear pore complex protein Nup93 / 93 kDa nucleoporin / An4a / Nucleoporin Nup93


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

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Protein , 9 types, 16 molecules BKCLDMENGPHQIRST

#2: Protein MGC154553 protein / outer Nup43


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 Nucleoporin SEH1-A / GATOR complex protein SEH1-A / Nup107-160 subcomplex subunit seh1-A


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 Nup160


Mass: 163103.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog)
#5: Protein MGC83926 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 GATOR complex protein SEC13 / Protein SEC13 homolog


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 Nuclear pore complex 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 outer Nup133


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 MGC83295 protein


Mass: 227854.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q642R6
#11: Protein Protein ELYS / Protein MEL-28 / xELYS


Mass: 268771.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q5U249

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: nuclear pore complex / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Xenopus laevis (African clawed frog)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 6000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 8.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 417490 / Symmetry type: POINT

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