7VOP

Cryo-EM structure of Xenopus laevis nuclear pore complex cytoplasmic ring subunit


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.2 of the entry. See complete history


Literature

8 angstrom structure of the outer rings of the Xenopus laevis nuclear pore complex obtained by cryo-EM and AI.

Tai, L.Zhu, Y.Ren, H.Huang, X.Zhang, C.Sun, F.

(2022) Protein Cell 13: 760-777

  • DOI: https://doi.org/10.1007/s13238-021-00895-y
  • Primary Citation of Related Structures:  
    7VCI, 7VOP

  • PubMed 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-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.


  • Organizational Affiliation

    National Key Laboratory of Biomacromolecules, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, 100101, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear pore complex protein Nup85
A, J
653Xenopus laevisMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MGC154553 protein
B, K
375Xenopus laevisMutation(s): 0 
UniProt
Find proteins for Q05AW3 (Xenopus laevis)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoporin SEH1-A
C, L
360Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoporin 160kDa
D, M
1,414Xenopus laevisMutation(s): 0 
UniProt
Find proteins for A0A6I8QA34 (Xenopus tropicalis)
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UniProt GroupA0A6I8QA34
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
MGC83926 protein
E, N
326Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear pore complex protein Nup96
F, O
924Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
GATOR complex protein SEC13
G, P
320Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear pore complex protein
H, Q
916Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
outer Nup133
I, R
1,140Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
MGC83295 protein
S, T
2,011Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear pore complex protein Nup93820Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Nup358
V, W, X, Y, Z
2,931Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoporin CANAA [auth a],
EA [auth e]
2,037Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Nup88A proteinBA [auth b],
DA [auth d]
728Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
IL4I1 proteinCA [auth c],
FA [auth f]
547Xenopus laevisMutation(s): 0 
UniProt
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release
  • Version 1.1: 2022-07-13
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection