1WWH

Crystal structure of the MPPN domain of mouse Nup35

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

The crystal structure of mouse Nup35 reveals atypical RNP motifs and novel homodimerization of the RRM domain

Handa, N., Kukimoto-Niino, M., Akasaka, R., Kishishita, S., Murayama, K., Terada, T., Inoue, M., Kigawa, T., Kose, S., Imamoto, N., Tanaka, A., Hayashizaki, Y., Shirouzu, M., Yokoyama, S.

(2006) J.Mol.Biol. 363: 114-124

  • DOI: 10.1016/j.jmb.2006.07.089

  • PubMed Abstract: 

    • The nuclear pore complex mediates the transport of macromolecules across the nuclear envelope (NE). The vertebrate nuclear pore protein Nup35, the ortholog of Saccharomyces cerevisiae Nup53p, is suggested to interact with the NE membrane and to be re ...

    The nuclear pore complex mediates the transport of macromolecules across the nuclear envelope (NE). The vertebrate nuclear pore protein Nup35, the ortholog of Saccharomyces cerevisiae Nup53p, is suggested to interact with the NE membrane and to be required for nuclear morphology. The highly conserved region between vertebrate Nup35 and yeast Nup53p is predicted to contain an RNA-recognition motif (RRM) domain. Due to its low level of sequence homology with other RRM domains, the RNP1 and RNP2 motifs have not been identified in its primary structure. In the present study, we solved the crystal structure of the RRM domain of mouse Nup35 at 2.7 A resolution. The Nup35 RRM domain monomer adopts the characteristic betaalphabetabetaalphabeta topology, as in other reported RRM domains. The structure allowed us to locate the atypical RNP1 and RNP2 motifs. Among the RNP motif residues, those on the beta-sheet surface are different from those of the canonical RRM domains, while those buried in the hydrophobic core are highly conserved. The RRM domain forms a homodimer in the crystal, in accordance with analytical ultracentrifugation experiments. The beta-sheet surface of the RRM domain, with its atypical RNP motifs, contributes to homodimerization mainly by hydrophobic interactions: the side-chain of Met236 in the beta4 strand of one Nup35 molecule is sandwiched by the aromatic side-chains of Phe178 in the beta1 strand and Trp209 in the beta3 strand of the other Nup35 molecule in the dimer. This structure reveals a new homodimerization mode of the RRM domain.

    Organizational Affiliation: 

    RIKEN Genomic Sciences Center, Tsurumi, Yokohama 230-0045, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
nucleoporin 35
A, B, C, D
119Mus musculusMutation(s): 0 
Gene Names: Nup35 (Mp44, Nup53)
Find proteins for Q8R4R6 (Mus musculus)
Go to UniProtKB:  Q8R4R6
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 59.486α = 90.00
b = 104.237β = 90.00
c = 110.039γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data reduction
CNSrefinement
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-07-05
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance