4J3H

Ring cycle for dilating and constricting the nuclear pore: structure of a Nup54 homo-tetramer.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5002 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Ring cycle for dilating and constricting the nuclear pore.

Solmaz, S.R.Blobel, G.Melcak, I.

(2013) Proc.Natl.Acad.Sci.USA 110: 5858-5863

  • DOI: 10.1073/pnas.1302655110

  • PubMed Abstract: 
  • We recently showed that the three "channel" nucleoporins, Nup54, Nup58, and Nup62, interact with each other through only four distinct sites and established the crystal structures of the two resulting "interactomes," Nup54•Nup58 and Nup54•Nup62. We a ...

    We recently showed that the three "channel" nucleoporins, Nup54, Nup58, and Nup62, interact with each other through only four distinct sites and established the crystal structures of the two resulting "interactomes," Nup54•Nup58 and Nup54•Nup62. We also reported instability of the Nup54•Nup58 interactome and previously determined the atomic structure of the relevant Nup58 segment by itself, demonstrating that it forms a twofold symmetric tetramer. Here, we report the crystal structure of the relevant free Nup54 segment and show that it forms a tetrameric, helical bundle that is structurally "conditioned" for instability by a central patch of polar hydrogen-bonded residues. Integrating these data with our previously reported results, we propose a "ring cycle" for dilating and constricting the nuclear pore. In essence, three homooligomeric rings, one consisting of eight modules of Nup58 tetramers, and two, each consisting of eight modules of Nup54 tetramers, are stacked in midplane and characterize a constricted pore of 10- to 20-nm diameter. In going to the dilated state, segments of one Nup58 and two Nup54 tetrameric modules reassort into a dodecameric module, eight of which form a single, heterooligomeric midplane ring, which is flexible in a diameter range of 40-50 nm. The ring cycle would be regulated by phenylalanine-glycine regions ("FG repeats") of channel nups. Akin to ligand-gated channels, the dilated state of the midplane ring may be stabilized by binding of [cargo•transport-factor] complexes to FG repeats, thereby linking the ratio of constricted to dilated nuclear pores to cellular transport need.


    Organizational Affiliation

    Laboratory of Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA. ssolmaz@rockefeller.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nuclear pore complex protein Nup54
A, B
46Rattus norvegicusMutation(s): 2 
Gene Names: Nup54
Find proteins for P70582 (Rattus norvegicus)
Go to UniProtKB:  P70582
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5002 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.192 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 41.320α = 90.00
b = 41.320β = 90.00
c = 198.410γ = 120.00
Software Package:
Software NamePurpose
PHENIXmodel building
XDSdata reduction
ADSCdata collection
PHENIXphasing
PHENIXrefinement
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-10
    Type: Initial release
  • Version 1.1: 2013-04-17
    Type: Database references, Structure summary