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: https://doi.org/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 . 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear pore complex protein Nup133A [auth AC],
BA [auth DC],
J [auth BC],
S [auth CC]
1,156Homo sapiensMutation(s): 0 
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PHAROS:  Q8WUM0
GTEx:  ENSG00000069248 
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UniProt GroupQ8WUM0
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear pore complex protein Nup107B [auth AD],
CA [auth DD],
K [auth BD],
T [auth CD]
925Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000111581 
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UniProt GroupP57740
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear pore complex protein Nup96C [auth AE],
DA [auth DE],
L [auth BE],
U [auth CE]
937Homo sapiensMutation(s): 0 
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PHAROS:  P52948
GTEx:  ENSG00000110713 
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UniProt GroupP52948
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Protein SEC13 homologD [auth AF],
EA [auth DF],
M [auth BF],
V [auth CF]
322Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000157020 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoporin SEH1E [auth AG],
FA [auth DG],
N [auth BG],
W [auth CG]
360Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000085415 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear pore complex protein Nup85F [auth AH],
GA [auth DH],
O [auth BH],
X [auth CH]
656Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125450 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoporin Nup43G [auth AI],
HA [auth DI],
P [auth BI],
Y [auth CI]
380Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000120253 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear pore complex protein Nup160H [auth AJ],
IA [auth DJ],
Q [auth BJ],
Z [auth CJ]
1,436Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000030066 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoporin Nup37AA [auth CK],
I [auth AK],
JA [auth DK],
R [auth BK]
326Homo sapiensMutation(s): 0 
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Find proteins for Q8NFH4 (Homo sapiens)
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PHAROS:  Q8NFH4
GTEx:  ENSG00000075188 
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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

View Full Validation Report



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