Multiple conformations in the ligand-binding site of the yeast nuclear pore targeting domain of NUP116P

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the lowest energy 

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This is version 1.4 of the entry. See complete history


Multiple Conformations in the Ligand-binding Site of the Yeast Nuclear Pore-targeting Domain of Nup116p

Robinson, M.A.Park, S.Sun, Z.-Y.J.Silver, P.A.Wagner, G.Hogle, J.M.

(2005) J Biol Chem 280: 35723-35732

  • DOI: https://doi.org/10.1074/jbc.M505068200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The yeast nucleoporin Nup116p plays an important role in mRNA export and protein transport. We have determined the solution structure of the C-terminal 147 residues of this protein, the region responsible for targeting the protein to the nuclear pore complex (NPC). The structure of Nup116p-C consists of a large beta-sheet sandwiched against a smaller one, flanked on both sides by alpha-helical stretches, similar to the structure of its human homolog, NUP98. In unliganded form, Nup116p-C exhibits evidence of exchange among multiple conformations, raising the intriguing possibility that it may adopt distinct conformations when bound to different partners in the NPC. We have additionally shown that a peptide from the N terminus of the nucleoporin Nup145p-C binds Nup116p-C. This previously unknown interaction may explain the unusual asymmetric localization pattern of Nup116p in the NPC. Strikingly, the exchange phenomenon observed in the unbound state is greatly reduced in the corresponding spectra of peptide-bound Nup116p-C, suggesting that the binding interaction stabilizes the domain conformation. This study offers a high resolution view of a yeast nucleoporin structural domain and may provide insights into NPC architecture and function.

  • Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
fragment of Nucleoporin NUP116/NSP116149Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NUP116NSP116
Find proteins for Q02630 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02630 
Go to UniProtKB:  Q02630
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02630
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-08-16
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-24
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.4: 2024-05-01
    Changes: Data collection, Database references