3TKN

Structure of the Nup82-Nup159-Nup98 heterotrimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.249 

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This is version 1.3 of the entry. See complete history


Literature

Molecular basis for the anchoring of proto-oncoprotein nup98 to the cytoplasmic face of the nuclear pore complex.

Stuwe, T.Schada von Borzyskowski, L.Davenport, A.M.Hoelz, A.

(2012) J Mol Biol 419: 330-346

  • DOI: https://doi.org/10.1016/j.jmb.2012.03.024
  • Primary Citation of Related Structures:  
    3TKN

  • PubMed Abstract: 

    The cytoplasmic filament nucleoporins of the nuclear pore complex (NPC) are critically involved in nuclear export and remodeling of mRNA ribonucleoprotein particles and are associated with various human malignancies. Here, we report the crystal structure of the Nup98 C-terminal autoproteolytic domain, frequently missing from leukemogenic forms of the protein, in complex with the N-terminal domain of Nup82 and the C-terminal tail fragment of Nup159. The Nup82 β propeller serves as a noncooperative binding platform for both binding partners. Interaction of Nup98 with Nup82 occurs through a reciprocal exchange of loop structures. Strikingly, the same Nup98 groove promiscuously interacts with Nup82 and Nup96 in a mutually excusive fashion. Simultaneous disruption of both Nup82 interactions in yeast causes severe defects in mRNA export, while the severing of a single interaction is tolerated. Thus, the cytoplasmic filament network of the NPC is robust, consistent with its essential function in nucleocytoplasmic transport.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoporin NUP82
A, D, G
452Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: HRB187J1135NUP82YJL061W
UniProt
Find proteins for P40368 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40368 
Go to UniProtKB:  P40368
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40368
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoporin NUP159
B, E, H
39Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NUP158NUP159RAT7YIL115C
UniProt
Find proteins for P40477 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40477 
Go to UniProtKB:  P40477
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40477
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoporin 98
C, F, I
152Mus musculusMutation(s): 0 
Gene Names: Nup98
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PFD9 (Mus musculus)
Explore Q6PFD9 
Go to UniProtKB:  Q6PFD9
IMPC:  MGI:109404
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6PFD9
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.249 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.905α = 90
b = 115.849β = 111.06
c = 118.488γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-11
    Type: Initial release
  • Version 1.1: 2012-04-18
    Changes: Database references
  • Version 1.2: 2012-06-06
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references