8TIE

Double nuclear outer ring of Nup84-complexes from the yeast NPC


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Implications of a multiscale structure of the yeast nuclear pore complex.

Akey, C.W.Echeverria, I.Ouch, C.Nudelman, I.Shi, Y.Wang, J.Chait, B.T.Sali, A.Fernandez-Martinez, J.Rout, M.P.

(2023) Mol Cell 83: 3283-3302.e5

  • DOI: https://doi.org/10.1016/j.molcel.2023.08.025
  • Primary Citation of Related Structures:  
    8T9L, 8TIE, 8TJ5

  • PubMed Abstract: 

    Nuclear pore complexes (NPCs) direct the nucleocytoplasmic transport of macromolecules. Here, we provide a composite multiscale structure of the yeast NPC, based on improved 3D density maps from cryogenic electron microscopy and AlphaFold2 models. Key features of the inner and outer rings were integrated into a comprehensive model. We resolved flexible connectors that tie together the core scaffold, along with equatorial transmembrane complexes and a lumenal ring that anchor this channel within the pore membrane. The organization of the nuclear double outer ring reveals an architecture that may be shared with ancestral NPCs. Additional connections between the core scaffold and the central transporter suggest that under certain conditions, a degree of local organization is present at the periphery of the transport machinery. These connectors may couple conformational changes in the scaffold to the central transporter to modulate transport. Collectively, this analysis provides insights into assembly, transport, and NPC evolution.


  • Organizational Affiliation

    Department of Pharmacology, Physiology and Biophysics, Boston University, Chobanian and Avedisian School of Medicine, 700 Albany Street, Boston, MA 02118, USA. Electronic address: cakey@bu.edu.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoporin NUP120A [auth a],
H [auth l]
1,037Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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UniProt GroupP35729
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoporin NUP85B [auth b],
I [auth m]
744Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P46673 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NUP145 isoform 1C [auth c],
J [auth n]
1,317Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P49687 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein SEC13D [auth d],
K [auth o]
297Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoporin Seh1E [auth e],
L [auth p]
307Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoporin NUP84F [auth f],
M [auth q]
726Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NUP133 isoform 1G [auth g],
N [auth r]
1,157Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P36161 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTMDFF
MODEL REFINEMENTCoot0.8.9.2
RECONSTRUCTIONcryoSPARC3.3.2

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)United StatesNIH R01 GM45377
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesNIH P41 GM109824
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesNIH R01 GM112108
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesNIH GM117212

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-11
    Type: Initial release