Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17.54 kDa 
• Atom Count: 1300 
• Residue Count: 151 
• Unique protein chains: 1

2Q5X

Crystal Structure of the C-terminal domain of hNup98

• DOI: 10.2210/pdb2Q5X/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.229 
• R-Value Work: 0.206 

Literature

Structural constraints on autoprocessing of the human nucleoporin Nup98.

Sun, Y., Guo, H.C.

(2008) Protein Sci 17: 494-505

• PubMed: 18287282 
• DOI: 10.1110/ps.073311808
• Primary Citation of Related Structures:  
  2Q5Y, 2Q5X


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear pore complex protein Nup98	A	155	Homo sapiens	Mutation(s): 1  Gene Names: NUP98, ADAR2 EC: 3.4.21
Find proteins for P52948 (Homo sapiens) Explore P52948  Go to UniProtKB:  P52948
NIH Common Fund Data Resources
PHAROS:  P52948 GTEx:  ENSG00000110713

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 69.674	α = 90
b = 69.674	β = 90
c = 90.964	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
DM	phasing
CNS	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
SOLVE	phasing

Structure Validation

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
  Changes: Version format compliance
• Version 1.2: 2017-10-18
  Changes: Advisory, Refinement description