3IKO

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.USA 106: 17693-17698

  • DOI: 10.1073/pnas.0909373106

  • 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 r ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein transport protein SEC13
A, D, G
297Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SEC13 (ANU3)
Find proteins for Q04491 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: SEC13
Go to UniProtKB:  Q04491
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nucleoporin NUP145C
B, E, H
442Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: NUP145 (RAT10)
EC: 3.4.21.-
Find proteins for P49687 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P49687
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Nucleoporin NUP84
C, F, I
460Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: NUP84
Find proteins for P52891 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P52891
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 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 = 90.00
b = 194.050β = 90.00
c = 327.806γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Advisory, Refinement description