3IKO

Crystal structure of the heterotrimeric Sec13-Nup145C-Nup84 nucleoporin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.234 

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This is version 1.3 of the entry. See complete history


Literature

Structure of a trimeric nucleoporin complex reveals alternate oligomerization states.

Nagy, V.Hsia, K.C.Debler, E.W.Kampmann, M.Davenport, A.M.Blobel, G.Hoelz, A.

(2009) Proc Natl Acad Sci U S A 106: 17693-17698

  • DOI: https://doi.org/10.1073/pnas.0909373106
  • Primary Citation of Related Structures:  
    3IKO

  • PubMed Abstract: 

    The heptameric Nup84 complex constitutes an evolutionarily conserved building block of the nuclear pore complex. Here, we present the crystal structure of the heterotrimeric Sec13 x Nup145C x Nup84 complex, the centerpiece of the heptamer, at 3.2-A resolution. Nup84 forms a U-shaped alpha-helical solenoid domain, topologically similar to two other members of the heptamer, Nup145C and Nup85. The interaction between Nup84 and Nup145C is mediated via a hydrophobic interface located in the kink regions of the two solenoids that is reinforced by additional interactions of two long Nup84 loops. The Nup84 binding site partially overlaps with the homo-dimerization interface of Nup145C, suggesting competing binding events. Fitting of the elongated Z-shaped heterotrimer into electron microscopy (EM) envelopes of the heptamer indicates that structural changes occur at the Nup145C x Nup84 interface. Docking the crystal structures of all heptamer components into the EM envelope constitutes a major advance toward the completion of the structural characterization of the Nup84 complex.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein SEC13
A, D, G
297Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SEC13ANU3YLR208WL8167.4
UniProt
Find proteins for Q04491 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q04491 
Go to UniProtKB:  Q04491
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04491
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoporin NUP145C
B, E, H
442Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NUP145RAT10YGL092W
EC: 3.4.21
UniProt
Find proteins for P49687 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P49687 
Go to UniProtKB:  P49687
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49687
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoporin NUP84
C, F, I
460Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NUP84YDL116W
UniProt
Find proteins for P52891 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P52891 
Go to UniProtKB:  P52891
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52891
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.397α = 90
b = 194.05β = 90
c = 327.806γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
SHARPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Advisory, Refinement description
  • Version 1.3: 2024-02-21
    Changes: Advisory, Data collection, Database references