7WB4

Cryo-EM structure of the NR subunit from X. laevis NPC


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Cryo-EM structure of the nuclear ring from Xenopus laevis nuclear pore complex.

Huang, G.Zhan, X.Zeng, C.Zhu, X.Liang, K.Zhao, Y.Wang, P.Wang, Q.Zhou, Q.Tao, Q.Liu, M.Lei, J.Yan, C.Shi, Y.

(2022) Cell Res 32: 349-358

  • DOI: https://doi.org/10.1038/s41422-021-00610-w
  • Primary Citation of Related Structures:  
    7WB4

  • PubMed Abstract: 

    Nuclear pore complex (NPC) shuttles cargo across the nuclear envelope. Here we present single-particle cryo-EM structure of the nuclear ring (NR) subunit from Xenopus laevis NPC at an average resolution of 5.6 Å. The NR subunit comprises two 10-membered Y complexes, each with the nucleoporin ELYS closely associating with Nup160 and Nup37 of the long arm. Unlike the cytoplasmic ring (CR) or inner ring (IR), the NR subunit contains only one molecule each of Nup205 and Nup93. Nup205 binds both arms of the Y complexes and interacts with the stem of inner Y complex from the neighboring subunit. Nup93 connects the stems of inner and outer Y complexes within the same NR subunit, and places its N-terminal extended helix into the axial groove of Nup205 from the neighboring subunit. Together with other structural information, we have generated a composite atomic model of the central ring scaffold that includes the NR, IR, and CR. The IR is connected to the two outer rings mainly through Nup155. This model facilitates functional understanding of vertebrate NPC.


  • Organizational Affiliation

    Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou, Zhejiang, China. huanggaoxingyu@westlake.edu.cn.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
outer Nup133A [auth J],
W [auth p],
X [auth j],
Y [auth P]
1,140Xenopus laevisMutation(s): 0 
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UniProt GroupA0A1L8H1I9
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear pore complex protein Nup85B,
F [auth b]
653Xenopus laevisMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
MGC154553 proteinC,
G [auth c]
375Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
MGC83926 proteinD [auth F],
J [auth f]
326Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoporin SEH1-BE [auth d],
T [auth D]
360Xenopus laevisMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
outer Nup160H [auth E],
I [auth e]
1,435Xenopus laevisMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Nup155-prov protein1,388Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
GATOR complex protein SEC13L [auth H],
N [auth h]
320Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear pore complex protein Nup96M [auth G],
O [auth g]
923Xenopus laevisMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear pore complex proteinP [auth I],
Q [auth i],
V [auth M]
916Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear pore complex protein Nup93R [auth L],
U [auth O]
820Xenopus laevisMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
MGC83295 proteinS [auth A]2,011Xenopus laevisMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Protein ELYSAA [auth N],
Z [auth n]
2,408Xenopus laevisMutation(s): 0 
UniProt
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2022-04-20
    Changes: Database references