4I9Y

Structure of the C-terminal domain of Nup358

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.125 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Structural and Functional Analysis of the C-Terminal Domain of Nup358/RanBP2.

Lin, D.H., Zimmermann, S., Stuwe, T., Stuwe, E., Hoelz, A.

(2013) J Mol Biol 425: 1318-1329

  • DOI: 10.1016/j.jmb.2013.01.021
  • Primary Citation of Related Structures:  
    4I9Y

  • PubMed Abstract: 

    • The nuclear pore complex is the sole mediator of bidirectional transport between the nucleus and cytoplasm. Nup358 is a metazoan-specific nucleoporin that localizes to the cytoplasmic filaments and provides several binding sites for the mobile nucleocytoplasmic transport machinery ...

    The nuclear pore complex is the sole mediator of bidirectional transport between the nucleus and cytoplasm. Nup358 is a metazoan-specific nucleoporin that localizes to the cytoplasmic filaments and provides several binding sites for the mobile nucleocytoplasmic transport machinery. Here we present the crystal structure of the C-terminal domain (CTD) of Nup358 at 1.75Å resolution. The structure reveals that the CTD adopts a cyclophilin-like fold with a non-canonical active-site configuration. We determined biochemically that the CTD possesses weak peptidyl-prolyl isomerase activity and show that the active-site cavity mediates a weak association with the human immunodeficiency virus-1 capsid protein, supporting its role in viral infection. Overall, the surface is evolutionarily conserved, suggesting that the CTD serves as a protein-protein interaction platform. However, we demonstrate that the CTD is dispensable for nuclear envelope localization of Nup358, suggesting that the CTD does not interact with other nucleoporins.

    Organizational Affiliation: 

    Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 SUMO-protein ligase RanBP2 A, B, C, D, E, F167Homo sapiensMutation(s): 0 
Gene Names: RANBP2, NUP358
EC: 2.3.2
Find proteins for P49792 (Homo sapiens)
Explore P49792 
Go to UniProtKB:  P49792
NIH Common Fund Data Resources
PHAROS:  P49792
GTEx:  ENSG00000153201
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TLA
Query on TLA
Download Ideal Coordinates CCD File 
A, B, E
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
A, B, C, D, E, F
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
A, B, C, D, E, F
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.125 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.062α = 90
b = 97.132β = 117.38
c = 108.151γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-30
    Type: Initial release
  • Version 1.1: 2013-02-13
    Changes: Database references
  • Version 1.2: 2013-04-24
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description