7N84

Double nuclear outer ring from the isolated yeast NPC


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Comprehensive structure and functional adaptations of the yeast nuclear pore complex.

Akey, C.W.Singh, D.Ouch, C.Echeverria, I.Nudelman, I.Varberg, J.M.Yu, Z.Fang, F.Shi, Y.Wang, J.Salzberg, D.Song, K.Xu, C.Gumbart, J.C.Suslov, S.Unruh, J.Jaspersen, S.L.Chait, B.T.Sali, A.Fernandez-Martinez, J.Ludtke, S.J.Villa, E.Rout, M.P.

(2022) Cell 185: 361-378.e25

  • DOI: 10.1016/j.cell.2021.12.015
  • Primary Citation of Related Structures:  
    7N84, 7N85, 7N9F

  • PubMed Abstract: 
  • Nuclear pore complexes (NPCs) mediate the nucleocytoplasmic transport of macromolecules. Here we provide a structure of the isolated yeast NPC in which the inner ring is resolved by cryo-EM at sub-nanometer resolution to show how flexible connectors tie together different structural and functional layers ...

    Nuclear pore complexes (NPCs) mediate the nucleocytoplasmic transport of macromolecules. Here we provide a structure of the isolated yeast NPC in which the inner ring is resolved by cryo-EM at sub-nanometer resolution to show how flexible connectors tie together different structural and functional layers. These connectors may be targets for phosphorylation and regulated disassembly in cells with an open mitosis. Moreover, some nucleoporin pairs and transport factors have similar interaction motifs, which suggests an evolutionary and mechanistic link between assembly and transport. We provide evidence for three major NPC variants that may foreshadow functional specializations at the nuclear periphery. Cryo-electron tomography extended these studies, providing a model of the in situ NPC with a radially expanded inner ring. Our comprehensive model reveals features of the nuclear basket and central transporter, suggests a role for the lumenal Pom152 ring in restricting dilation, and highlights structural plasticity that may be required for transport.


    Organizational Affiliation

    Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA. Electronic address: rout@rockefeller.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin NUP188A [auth X]1,655Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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UniProt GroupP52593
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
unknownB [auth Y],
C [auth Z]
63Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin NUP120D [auth a],
K [auth l]
1,037Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin NUP85E [auth b],
L [auth m]
744Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin 145cF [auth c],
M [auth n]
712Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.21
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Protein transport protein SEC13G [auth d],
N [auth o]
297Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin SEH1H [auth e],
O [auth p]
349Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin NUP84I [auth f],
P [auth q]
726Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin NUP133J [auth g],
Q [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: 11.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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 StatesR01 GM45377
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM112108
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41 GM109824

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-26
    Type: Initial release
  • Version 1.1: 2022-02-02
    Changes: Database references, Derived calculations