3LCN

Nab2:Gfd1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for the function of the Saccharomyces cerevisiae Gfd1 protein in mRNA nuclear export.

Zheng, C.Fasken, M.B.Marshall, N.J.Brockmann, C.Rubinson, M.E.Wente, S.R.Corbett, A.H.Stewart, M.

(2010) J.Biol.Chem. 285: 20704-20715

  • DOI: 10.1074/jbc.M110.107276

  • PubMed Abstract: 
  • Following transcription, mRNA is processed, packaged into messenger ribonucleoprotein (mRNP) particles, and transported through nuclear pores (NPCs) to the cytoplasm. At the NPC cytoplasmic face, Dbp5 mediates mRNP remodeling and mRNA export factor d ...

    Following transcription, mRNA is processed, packaged into messenger ribonucleoprotein (mRNP) particles, and transported through nuclear pores (NPCs) to the cytoplasm. At the NPC cytoplasmic face, Dbp5 mediates mRNP remodeling and mRNA export factor dissociation, releasing transcripts for translation. In Saccharomyces cerevisiae, the conserved poly(A) RNA-binding protein, Nab2, facilitates NPC targeting of transcripts and also modulates poly(A) tail length. Dbp5 removes Nab2 from mRNPs at the cytoplasmic face of the pore and, importantly, a Nab2 RNA-binding mutant suppresses the thermosensitive rat8-2 (dbp5) mutant. GFD1 is a multicopy suppressor of rat8-2 (dbp5), and Gfd1 interacts physically with both Dbp5 and the Nab2 N-terminal domain (Nab2-N). Here, we present a structural and functional analysis of the Gfd1/Nab2-N interaction. Crystallography, supported by solution NMR, shows that Gfd1 residues 126-150 form an alpha-helix when bound to Nab2-N. Engineered Nab2-N and Gfd1 mutants that inhibit this interaction in vitro were used to probe its function in vivo using the genetic interaction between GFD1 and NAB2. Although GFD1 is not essential for viability, its deletion severely impairs growth of rat8-2 (dbp5) cells. Moreover, although Gfd1 overexpression suppresses rat8-2 (dbp5), Gfd1 mutants that do not bind Nab2 only partially suppress rat8-2 (dbp5). Furthermore, rat8-2 (dbp5) cells that express nab2-Y34A, in which binding to Gfd1 is impaired, show a synthetic growth phenotype and nuclear accumulation of poly(A) RNA. These data support the importance of the Gfd1/Nab2 interaction for Dbp5 activity and provide further molecular details of the interactions that facilitate Dbp5-mediated mRNP remodeling in the terminal step of mRNA export.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nuclear polyadenylated RNA-binding protein NAB2
A, B
105Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: NAB2
Find proteins for P32505 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: NAB2
Go to UniProtKB:  P32505
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
mRNA transport factor GFD1
C, D
29Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: GFD1
Find proteins for Q04839 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q04839
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 55.833α = 90.00
b = 121.762β = 90.00
c = 37.376γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHASERphasing
SCALAdata scaling
ADSCdata collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-01-11 
  • Released Date: 2010-05-12 
  • Deposition Author(s): Stewart, M.

Revision History 

  • Version 1.0: 2010-05-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance