6LK8

Structure of Xenopus laevis Cytoplasmic Ring subunit.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.50 Å
  • Aggregation State: TISSUE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structure of the cytoplasmic ring of the Xenopus laevis nuclear pore complex by cryo-electron microscopy single particle analysis.

Huang, G.Zhang, Y.Zhu, X.Zeng, C.Wang, Q.Zhou, Q.Tao, Q.Liu, M.Lei, J.Yan, C.Shi, Y.

(2020) Cell Res 30: 520-531

  • DOI: 10.1038/s41422-020-0319-4
  • Primary Citation of Related Structures:  
    6LK8

  • PubMed Abstract: 
  • The nuclear pore complex (NPC) exhibits structural plasticity and has only been characterized at local resolutions of up to 15 Å for the cytoplasmic ring (CR). Here we present a single-particle cryo-electron microscopy (cryo-EM) structure of the CR from Xenopus laevis NPC at average resolutions of 5 ...

    The nuclear pore complex (NPC) exhibits structural plasticity and has only been characterized at local resolutions of up to 15 Å for the cytoplasmic ring (CR). Here we present a single-particle cryo-electron microscopy (cryo-EM) structure of the CR from Xenopus laevis NPC at average resolutions of 5.5-7.9 Å, with local resolutions reaching 4.5 Å. Improved resolutions allow identification and placement of secondary structural elements in the majority of the CR components. The two Y complexes in each CR subunit interact with each other and associate with those from flanking subunits, forming a circular scaffold. Within each CR subunit, the Nup358-containing region wraps around the stems of both Y complexes, likely stabilizing the scaffold. Nup205 connects the short arms of the two Y complexes and associates with the stem of a neighboring Y complex. The Nup214-containing region uses an extended coiled-coil to link Nup85 of the two Y complexes and protrudes into the axial pore of the NPC. These previously uncharacterized structural features reveal insights into NPC assembly.


    Organizational Affiliation

    Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China. syg@westlake.edu.cn.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MGC83295 proteinA, W [auth a]2011Xenopus laevisMutation(s): 0 
Gene Names: nup205.SMGC83295nup205
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear pore complex protein Nup85B, X [auth b]653Xenopus laevisMutation(s): 0 
Gene Names: nup85
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
MGC154553 proteinC, Y [auth c]375Xenopus laevisMutation(s): 0 
Gene Names: nup43.SMGC154553nup43
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin SEH1-AD, Z [auth d]322Xenopus laevisMutation(s): 0 
Gene Names: seh1l-a
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
outer Nup160E, AA [auth e]1435Xenopus laevisMutation(s): 0 
Gene Names: XELAEV_18021930mg
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
MGC83926 proteinF, BA [auth f]326Xenopus laevisMutation(s): 0 
Gene Names: nup37.LMGC83926nup37XELAEV_18017377mg
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear pore complex protein Nup96G, CA [auth g]923Xenopus laevisMutation(s): 0 
Gene Names: XELAEV_18016499mg
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
GATOR complex protein SEC13H, DA [auth h]320Xenopus laevisMutation(s): 0 
Gene Names: sec13.Ssec13sec13l1XELAEV_18025861mg
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear pore complex proteinI, EA [auth i]916Xenopus laevisMutation(s): 0 
Gene Names: nup107.SLOC100037138nup107XELAEV_18021181mg
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
outer Nup133J, FA [auth j]1140Xenopus laevisMutation(s): 0 
Gene Names: nup133.LXELAEV_18018579mg
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Nup358 complex, clampsK [auth S], L [auth T], M [auth U], N [auth V]2905Xenopus laevisMutation(s): 0 
Gene Names: ranbp2.Lranbp2XELAEV_18012918mg
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Nup214 complex Coiled-coil region 1, helix 1O [auth K]69Xenopus laevisMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Nup214 complex coiled coil region 1, helix 2P [auth L]80Xenopus laevisMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Nup214 complex coiled coil region 1, helix 3Q [auth M]73Xenopus laevisMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Nup214 complex Coiled coil region 2, helix 1R [auth N]31Xenopus laevisMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Nup214 complex Coiled coil region 2, helix 2S [auth O]35Xenopus laevisMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Nup214 complex Coiled coil region 2, helix 3T [auth P]26Xenopus laevisMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
bridge domainU [auth Q], V [auth R]391Xenopus laevisMutation(s): 0 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.50 Å
  • Aggregation State: TISSUE 
  • 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)China31430020
National Natural Science Foundation of China (NSFC)China31621092

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-21
    Type: Initial release