Crystal structure of the C-terminal domain of nuclear pore complex component NUP116 from Candida glabrata

Experimental Data Snapshot

  • Resolution: 1.94 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

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Atomic structure of the nuclear pore complex targeting domain of a Nup116 homologue from the yeast, Candida glabrata.

Sampathkumar, P.Kim, S.J.Manglicmot, D.Bain, K.T.Gilmore, J.Gheyi, T.Phillips, J.Pieper, U.Fernandez-Martinez, J.Franke, J.D.Matsui, T.Tsuruta, H.Atwell, S.Thompson, D.A.Emtage, J.S.Wasserman, S.R.Rout, M.P.Sali, A.Sauder, J.M.Almo, S.C.Burley, S.K.

(2012) Proteins 80: 2110-2116

  • DOI: https://doi.org/10.1002/prot.24102
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The nuclear pore complex (NPC), embedded in the nuclear envelope, is a large, dynamic molecular assembly that facilitates exchange of macromolecules between the nucleus and the cytoplasm. The yeast NPC is an eightfold symmetric annular structure composed of ~456 polypeptide chains contributed by ~30 distinct proteins termed nucleoporins. Nup116, identified only in fungi, plays a central role in both protein import and mRNA export through the NPC. Nup116 is a modular protein with N-terminal "FG" repeats containing a Gle2p-binding sequence motif and a NPC targeting domain at its C-terminus. We report the crystal structure of the NPC targeting domain of Candida glabrata Nup116, consisting of residues 882-1034 [CgNup116(882-1034)], at 1.94 Å resolution. The X-ray structure of CgNup116(882-1034) is consistent with the molecular envelope determined in solution by small-angle X-ray scattering. Structural similarities of CgNup116(882-1034) with homologous domains from Saccharomyces cerevisiae Nup116, S. cerevisiae Nup145N, and human Nup98 are discussed.

  • Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA. psampath@aecom.yu.edu

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoporin NUP116
A, B
164Nakaseomyces glabratusMutation(s): 0 
Gene Names: CAGL0F06171gNUP116 (gi50287617)
Find proteins for Q6FU56 (Candida glabrata (strain ATCC 2001 / BCRC 20586 / JCM 3761 / NBRC 0622 / NRRL Y-65 / CBS 138))
Explore Q6FU56 
Go to UniProtKB:  Q6FU56
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6FU56
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 1.94 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.703α = 90
b = 67.668β = 101.37
c = 55.119γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-12-21
    Changes: Structure summary
  • Version 1.3: 2012-06-20
    Changes: Database references
  • Version 1.4: 2012-10-10
    Changes: Database references
  • Version 1.5: 2018-11-21
    Changes: Data collection, Structure summary
  • Version 1.6: 2021-02-10
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.7: 2023-09-06
    Changes: Data collection, Database references, Refinement description
  • Version 1.8: 2023-11-22
    Changes: Data collection