Crystal Structure of a Nucleoporin

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

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Structure and nucleic acid binding activity of the nucleoporin Nup157.

Seo, H.S.Blus, B.J.Jankovic, N.Z.Blobel, G.

(2013) Proc Natl Acad Sci U S A 110: 16450-16455

  • DOI: https://doi.org/10.1073/pnas.1316607110
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    At the center of the nuclear pore complex (NPC) is a uniquely versatile central transport channel. Structural analyses of distinct segments ("protomers") of the three "channel" nucleoporins yielded a model for how this channel is constructed. Its principal feature is a midplane ring that can undergo regulated diameter changes of as much as an estimated 30 nm. To better understand how a family of "adaptor" nucleoporins--concentrically surrounding this channel--might cushion these huge structural changes, we determined the crystal structure of one adaptor nucleoporin, Nup157. Here, we show that a recombinant Saccharomyces cerevisiae Nup157 protomer, representing two-thirds of Nup157 (residues 70-893), folds into a seven-bladed β-propeller followed by an α-helical domain, which together form a C-shaped architecture. Notably, the structure contains a large patch of positively charged residues, most of which are evolutionarily conserved. Consistent with this surface feature, we found that Nup157(70-893) binds to nucleic acids, although in a sequence-independent manner. Nevertheless, this interaction supports a previously reported role of Nup157, and its paralogue Nup170, in chromatin organization. Based on its nucleic acid binding capacity, we propose a dual location and function of Nup157. Finally, modeling the remaining C-terminal portion of Nup157 shows that it projects as a superhelical stack from the compact C-shaped portion of the molecule. The predicted four hinge regions indicate an intrinsic flexibility of Nup157, which could contribute to structural plasticity within the NPC.

  • Organizational Affiliation

    Laboratory of Cell Biology and Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoporin NUP157826Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NUP157YER105C
Find proteins for P40064 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40064 
Go to UniProtKB:  P40064
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40064
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.11α = 90
b = 76.94β = 106.05
c = 82.63γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
PHENIXmodel building
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-25
    Type: Initial release
  • Version 1.1: 2013-10-09
    Changes: Database references
  • Version 1.2: 2013-10-23
    Changes: Database references