7PEQ

Model of the outer rings of the human nuclear pore complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 35.0 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The cellular environment shapes the nuclear pore complex architecture.

Schuller, A.P.Wojtynek, M.Mankus, D.Tatli, M.Kronenberg-Tenga, R.Regmi, S.G.Dip, P.V.Lytton-Jean, A.K.R.Brignole, E.J.Dasso, M.Weis, K.Medalia, O.Schwartz, T.U.

(2021) Nature 598: 667-671

  • DOI: 10.1038/s41586-021-03985-3
  • Primary Citation of Related Structures:  
    7PEQ, 7PER

  • PubMed Abstract: 
  • Nuclear pore complexes (NPCs) create large conduits for cargo transport between the nucleus and cytoplasm across the nuclear envelope (NE) 1-3 . These multi-megadalton structures are composed of about thirty different nucleoporins that are distributed in three main substructures (the inner, cytoplasmic and nucleoplasmic rings) around the central transport channel 4-6 ...

    Nuclear pore complexes (NPCs) create large conduits for cargo transport between the nucleus and cytoplasm across the nuclear envelope (NE) 1-3 . These multi-megadalton structures are composed of about thirty different nucleoporins that are distributed in three main substructures (the inner, cytoplasmic and nucleoplasmic rings) around the central transport channel 4-6 . Here we use cryo-electron tomography on DLD-1 cells that were prepared using cryo-focused-ion-beam milling to generate a structural model for the human NPC in its native environment. We show that-compared with previous human NPC models obtained from purified NEs-the inner ring in our model is substantially wider; the volume of the central channel is increased by 75% and the nucleoplasmic and cytoplasmic rings are reorganized. Moreover, the NPC membrane exhibits asymmetry around the inner-ring complex. Using targeted degradation of Nup96, a scaffold nucleoporin of the cytoplasmic and nucleoplasmic rings, we observe the interdependence of each ring in modulating the central channel and maintaining membrane asymmetry. Our findings highlight the inherent flexibility of the NPC and suggest that the cellular environment has a considerable influence on NPC dimensions and architecture.


    Organizational Affiliation

    Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. tus@mit.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear pore complex protein Nup133A [auth AC], J [auth BC], S [auth CC], BA [auth DC]1156Homo sapiensMutation(s): 0 
Gene Names: NUP133
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PHAROS:  Q8WUM0
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear pore complex protein Nup107B [auth AD], K [auth BD], T [auth CD], CA [auth DD]925Homo sapiensMutation(s): 0 
Gene Names: NUP107
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear pore complex protein Nup96C [auth AE], L [auth BE], U [auth CE], DA [auth DE]937Homo sapiensMutation(s): 0 
Gene Names: NUP98ADAR2
EC: 3.4.21
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Protein SEC13 homologD [auth AF], M [auth BF], V [auth CF], EA [auth DF]322Homo sapiensMutation(s): 0 
Gene Names: SEC13D3S1231ESEC13ASEC13L1SEC13R
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin SEH1E [auth AG], N [auth BG], W [auth CG], FA [auth DG]360Homo sapiensMutation(s): 0 
Gene Names: SEH1LSEC13LSEH1
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear pore complex protein Nup85F [auth AH], O [auth BH], X [auth CH], GA [auth DH]656Homo sapiensMutation(s): 0 
Gene Names: NUP85NUP75PCNT1
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin Nup43G [auth AI], P [auth BI], Y [auth CI], HA [auth DI]380Homo sapiensMutation(s): 0 
Gene Names: NUP43
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear pore complex protein Nup160H [auth AJ], Q [auth BJ], Z [auth CJ], IA [auth DJ]1436Homo sapiensMutation(s): 0 
Gene Names: NUP160KIAA0197NUP120
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin Nup37I [auth AK], R [auth BK], AA [auth CK], JA [auth DK]326Homo sapiensMutation(s): 0 
Gene Names: NUP37
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 35.0 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)SwitzerlandR01-GM77537
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)SwitzerlandR35-GM141834
Swiss National Science FoundationSwitzerlandSNSF 31003A_179418

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-20
    Type: Initial release
  • Version 1.1: 2021-10-27
    Changes: Data collection, Database references
  • Version 1.2: 2021-11-10
    Changes: Data collection, Database references
  • Version 1.3: 2021-11-17
    Changes: Data collection, Database references
  • Version 1.4: 2021-11-24
    Changes: Data collection, Database references