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 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.5 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WUM0 (Homo sapiens)
Explore Q8WUM0 
Go to UniProtKB:  Q8WUM0
PHAROS:  Q8WUM0
GTEx:  ENSG00000069248 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WUM0
Sequence Annotations
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  • Reference Sequence
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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 
UniProt & NIH Common Fund Data Resources
Find proteins for P57740 (Homo sapiens)
Explore P57740 
Go to UniProtKB:  P57740
PHAROS:  P57740
GTEx:  ENSG00000111581 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP57740
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  • Reference Sequence
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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 
EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for P52948 (Homo sapiens)
Explore P52948 
Go to UniProtKB:  P52948
PHAROS:  P52948
GTEx:  ENSG00000110713 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52948
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  • Reference Sequence
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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 
UniProt & NIH Common Fund Data Resources
Find proteins for P55735 (Homo sapiens)
Explore P55735 
Go to UniProtKB:  P55735
PHAROS:  P55735
GTEx:  ENSG00000157020 
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UniProt GroupP55735
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  • Reference Sequence
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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 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96EE3 (Homo sapiens)
Explore Q96EE3 
Go to UniProtKB:  Q96EE3
PHAROS:  Q96EE3
GTEx:  ENSG00000085415 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96EE3
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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 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BW27 (Homo sapiens)
Explore Q9BW27 
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PHAROS:  Q9BW27
GTEx:  ENSG00000125450 
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UniProt GroupQ9BW27
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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 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NFH3 (Homo sapiens)
Explore Q8NFH3 
Go to UniProtKB:  Q8NFH3
PHAROS:  Q8NFH3
GTEx:  ENSG00000120253 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NFH3
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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 
UniProt & NIH Common Fund Data Resources
Find proteins for Q12769 (Homo sapiens)
Explore Q12769 
Go to UniProtKB:  Q12769
PHAROS:  Q12769
GTEx:  ENSG00000030066 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12769
Sequence Annotations
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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 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NFH4 (Homo sapiens)
Explore Q8NFH4 
Go to UniProtKB:  Q8NFH4
PHAROS:  Q8NFH4
GTEx:  ENSG00000075188 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NFH4
Sequence Annotations
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  • Reference Sequence
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
  • Version 1.5: 2024-07-17
    Changes: Data collection, Derived calculations, Refinement description
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