2Q5Y

Crystal Structure of the C-terminal domain of hNup98


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural constraints on autoprocessing of the human nucleoporin Nup98.

Sun, Y.Guo, H.C.

(2008) Protein Sci. 17: 494-505

  • DOI: 10.1110/ps.073311808
  • Primary Citation of Related Structures:  

  • 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 t ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nuclear pore complex protein Nup98
A, C
152Homo sapiensMutation(s): 0 
Gene Names: NUP98 (ADAR2)
EC: 3.4.21.-
Find proteins for P52948 (Homo sapiens)
Go to Gene View: NUP98
Go to UniProtKB:  P52948
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear pore complex protein Nup96
B, D
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.228 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 90.301α = 90.00
b = 90.301β = 90.00
c = 97.648γ = 120.00
Software Package:
Software NamePurpose
DMphasing
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
PDB_EXTRACTdata extraction
CNSrefinement
CBASSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-06-03 
  • Released Date: 2008-10-14 
  • Deposition Author(s): Sun, Y., Guo, H.C.

Revision History 

  • Version 1.0: 2008-10-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-18
    Type: Advisory, Refinement description