4GA1 | pdb_00004ga1

Structure of the N-terminal domain of Nup358

• PDB DOI: https://doi.org/10.2210/pdb4GA1/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Pan troglodytes
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-07-24 Released: 2012-09-26 
• Deposition Author(s): Hoelz, A., Kassube, S.A., Lin, D.H., Stuwe, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 
  0.223 (Depositor), 0.393 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.390 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

Crystal structure of the N-terminal domain of Nup358/RanBP2.

Kassube, S.A., Stuwe, T., Lin, D.H., Antonuk, C.D., Napetschnig, J., Blobel, G., Hoelz, A.

(2012) J Mol Biology 423: 752-765

• PubMed: 22959972 
• DOI: https://doi.org/10.1016/j.jmb.2012.08.026
• Primary Citation Related Structures: 
  4GA0, 4GA1, 4GA2


• PubMed Abstract: 
  

  Key steps in mRNA export are the nuclear assembly of messenger ribonucleoprotein particles (mRNPs), the translocation of mRNPs through the nuclear pore complex (NPC), and the mRNP remodeling events at the cytoplasmic side of the NPC. Nup358/RanBP2 is a constituent of the cytoplasmic filaments of the NPC specific to higher eukaryotes and provides a multitude of binding sites for the nucleocytoplasmic transport machinery. Here, we present the crystal structure of the Nup358 N-terminal domain (NTD) at 0.95Å resolution. The structure reveals an α-helical domain that harbors three central tetratricopeptide repeats (TPRs), flanked on each side by an additional solvating amphipathic α helix. Overall, the NTD adopts an unusual extended conformation that lacks the characteristic peptide-binding groove observed in canonical TPR domains. Strikingly, the vast majority of the NTD surface exhibits an evolutionarily conserved, positive electrostatic potential, and we demonstrate that the NTD possesses the capability to bind single-stranded RNA in solution. Together, these data suggest that the NTD contributes to mRNP remodeling events at the cytoplasmic face of the NPC.

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Organizational Affiliation: 
• Laboratory of Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 17.51 kDa 
• Atom Count: 1,434 
• Modeled Residue Count: 143 
• Deposited Residue Count: 150 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 SUMO-PROTEIN LIGASE RANBP2	A	150	Pan troglodytes	Mutation(s): 3  Gene Names: ENSG00000153201 EC: 2.3.2
UniProt
Find proteins for H2QII6 (Pan troglodytes) Explore H2QII6  Go to UniProtKB:  H2QII6

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free:  0.223 (Depositor), 0.393 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.390 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.387	α = 90
b = 83.641	β = 90
c = 29.984	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-26 
Deposition Author(s): Hoelz, A., Kassube, S.A., Lin, D.H., Stuwe, T.

Revision History  

• Version 1.0: 2012-09-26
  Type: Initial release
  
• Version 1.1: 2013-01-02
  Changes: Database references
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary