Structure of the C-terminal domain of Nup358

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.125 

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This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1016/j.jmb.2013.01.021
  • Primary Citation of Related Structures:  

  • 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. 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 SUMO-protein ligase RanBP2
A, B, C, D, E
A, B, C, D, E, F
167Homo sapiensMutation(s): 0 
Gene Names: RANBP2NUP358
UniProt & NIH Common Fund Data Resources
Find proteins for P49792 (Homo sapiens)
Explore P49792 
Go to UniProtKB:  P49792
PHAROS:  P49792
GTEx:  ENSG00000153201 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49792
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on TLA

Download Ideal Coordinates CCD File 
EA [auth E],
J [auth A],
Q [auth B]
C4 H6 O6
Query on GOL

Download Ideal Coordinates CCD File 
BA [auth D]
CA [auth E]
FA [auth E]
G [auth A]
GA [auth F]
BA [auth D],
CA [auth E],
FA [auth E],
G [auth A],
GA [auth F],
H [auth A],
HA [auth F],
JA [auth F],
K [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
R [auth B],
S [auth C],
T [auth C],
V [auth C],
W [auth D],
X [auth D],
Y [auth D],
Z [auth D]
C3 H8 O3
Query on CL

Download Ideal Coordinates CCD File 
AA [auth D]
DA [auth E]
I [auth A]
IA [auth F]
P [auth B]
AA [auth D],
DA [auth E],
I [auth A],
IA [auth F],
P [auth B],
U [auth C]
Experimental Data & Validation

Experimental Data

  • 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
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling

Structure Validation

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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