7WKK

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.1 of the entry. See complete history


Literature

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

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

(2022) Cell Res 32: 451-460

  • DOI: 10.1038/s41422-022-00633-x
  • Primary Citation of Related Structures:  
    7WKK

  • PubMed Abstract: 
  • Nuclear pore complex (NPC) mediates nucleocytoplasmic shuttling. Here we present single-particle cryo-electron microscopy structure of the inner ring (IR) subunit from the Xenopus laevis NPC at an average resolution of 4.2 Å. A homo-dimer of Nup205 resides at the center of the IR subunit, flanked by two molecules of Nup188 ...

    Nuclear pore complex (NPC) mediates nucleocytoplasmic shuttling. Here we present single-particle cryo-electron microscopy structure of the inner ring (IR) subunit from the Xenopus laevis NPC at an average resolution of 4.2 Å. A homo-dimer of Nup205 resides at the center of the IR subunit, flanked by two molecules of Nup188. Four molecules of Nup93 each places an extended helix into the axial groove of Nup205 or Nup188, together constituting the central scaffold. The channel nucleoporin hetero-trimer of Nup62/58/54 is anchored on the central scaffold. Six Nup155 molecules interact with the central scaffold and together with the NDC1-ALADIN hetero-dimers anchor the IR subunit to the nuclear envelope and to outer rings. The scarce inter-subunit contacts may allow sufficient latitude in conformation and diameter of the IR. Our structure reveals the molecular basis for the IR subunit assembly of a vertebrate NPC.


    Organizational Affiliation

    Tsinghua University-Peking University Joint Center for Life Sciences; School of Life Sciences, Tsinghua University, Beijing, China. syg@westlake.edu.cn.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MGC83295 proteinA,
N [auth a]
2,011Xenopus laevisMutation(s): 0 
Gene Names: nup205.SMGC83295nup205nup205.Lxnup205
UniProt
Find proteins for Q642R6 (Xenopus laevis)
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UniProt GroupQ642R6
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nup188 domain-containing proteinB,
O [auth b]
1,739Xenopus laevisMutation(s): 0 
Gene Names: nup188.S
UniProt
Find proteins for A0A1L8F1N1 (Xenopus laevis)
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UniProt GroupA0A1L8F1N1
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear pore complex protein Nup93C,
E,
P [auth c],
R [auth e]
820Xenopus laevisMutation(s): 0 
Gene Names: nup93
UniProt
Find proteins for Q7ZX96 (Xenopus laevis)
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UniProt GroupQ7ZX96
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Nup155-prov protein1,388Xenopus laevisMutation(s): 0 
Gene Names: nup155.Lnup155
UniProt
Find proteins for Q7ZWL0 (Xenopus laevis)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Nup54G,
J,
T [auth g],
W [auth j]
535Xenopus laevisMutation(s): 0 
Gene Names: nup54.Snup54
UniProt
Find proteins for K9ZTJ6 (Xenopus laevis)
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UniProt GroupK9ZTJ6
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
IL4I1 proteinH,
K [auth L],
U [auth h],
X [auth l]
547Xenopus laevisMutation(s): 0 
Gene Names: nup62.LibsnIL4I1il4i1nup62p62sndi
UniProt
Find proteins for Q91349 (Xenopus laevis)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
MGC84997 proteinI,
L [auth K],
V [auth i],
Y [auth k]
599Xenopus laevisMutation(s): 0 
Gene Names: nup58.SMGC84997nup58nupl1pro2463
UniProt
Find proteins for Q5EAX5 (Xenopus laevis)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Aaas-prov proteinAA [auth O],
CA [auth o]
523Xenopus laevisMutation(s): 0 
Gene Names: aaas.Laaasaaas-prov
UniProt
Find proteins for Q6DCM0 (Xenopus laevis)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin NDC1BA [auth N],
DA [auth n]
660Xenopus laevisMutation(s): 0 
Gene Names: ndc1tmem48
UniProt
Find proteins for Q6AX31 (Xenopus laevis)
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UniProt GroupQ6AX31
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 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: 2022-03-30
    Type: Initial release
  • Version 1.1: 2022-05-18
    Changes: Database references