Crystal Structure of the C-terminal domain of hNup98

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.206 

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This is version 1.4 of the entry. See complete history


Structural constraints on autoprocessing of the human nucleoporin Nup98.

Sun, Y.Guo, H.C.

(2008) Protein Sci 17: 494-505

  • DOI: https://doi.org/10.1110/ps.073311808
  • Primary Citation of Related Structures:  
    2Q5X, 2Q5Y

  • PubMed Abstract: 

    Nucleoporin Nup98, a 98-kDa protein component of the nuclear pore complex, plays an important role in both protein and RNA transport. During its maturation process, Nup98 undergoes post-translational autoproteolysis, which is critical for targeting to the NPC. Here we present high-resolution crystal structures of the C-terminal autoproteolytic domains of Nup98 (2.3 A for the wild type and 1.9 A for the S864A precursor), and propose a detailed autoproteolysis mechanism through an N-O acyl shift. Structural constraints are found at the autocleavage site, and could thus provide a driving force for autocleavage at the scissile peptide bond. Such structural constraints appear to be generated, at least in part, by anchoring a conserved phenylalanine side chain into a highly conserved hydrophobic pocket at the catalytic site. Our high-resolution crystal structures also reveal that three highly conserved residues, Tyr866, Gly867, and Leu868, provide most of the interactions between the autoproteolytic domain and the C-terminal tail. These results suggest that Nup98 may represent a new subtype of protein that utilizes autoprocessing to control biogenesis pathways and intracellular translocation.

  • Organizational Affiliation

    Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts 02118-2526, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear pore complex protein Nup98155Homo sapiensMutation(s): 1 
Gene Names: NUP98
UniProt & NIH Common Fund Data Resources
Find proteins for P52948 (Homo sapiens)
Explore P52948 
Go to UniProtKB:  P52948
PHAROS:  P52948
GTEx:  ENSG00000110713 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52948
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.206 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.674α = 90
b = 69.674β = 90
c = 90.964γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CBASSdata collection

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-18
    Changes: Advisory, Refinement description
  • Version 1.3: 2021-10-20
    Changes: Advisory, Database references
  • Version 1.4: 2024-02-21
    Changes: Data collection