4OWR

Vesiculoviral matrix (M) protein occupies nucleic acid binding site at nucleoporin pair Rae1-Nup98


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Vesiculoviral matrix (M) protein occupies nucleic acid binding site at nucleoporin pair (Rae1 Nup98).

Quan, B.Seo, H.S.Blobel, G.Ren, Y.

(2014) Proc.Natl.Acad.Sci.USA 111: 9127-9132

  • DOI: 10.1073/pnas.1409076111

  • PubMed Abstract: 
  • mRNA export factor 1 (Rae1) and nucleoporin 98 (Nup98) are host cell targets for the matrix (M) protein of vesicular stomatitis virus (VSV). How Rae1 functions in mRNA export and how M protein targets both Rae1 and Nup98 are not understood at the mol ...

    mRNA export factor 1 (Rae1) and nucleoporin 98 (Nup98) are host cell targets for the matrix (M) protein of vesicular stomatitis virus (VSV). How Rae1 functions in mRNA export and how M protein targets both Rae1 and Nup98 are not understood at the molecular level. To obtain structural insights, we assembled a 1:1:1 complex of M•Rae1•Nup98 and established a crystal structure at 3.15-Å resolution. We found that the M protein contacts the Rae1•Nup98 heterodimer principally by two protrusions projecting from the globular domain of M like a finger and thumb. Both projections clamp to the side of the β-propeller of Rae1, with the finger also contacting Nup98. The most prominent feature of the finger is highly conserved Methionine 51 (Met51) with upstream and downstream acidic residues. The complementary surface on Rae1 displays a deep hydrophobic pocket, into which Met51 fastens like a bolt, and a groove of basic residues on either side, which bond to the acidic residues of the finger. Notably, the M protein competed for in vitro binding of various oligonucleotides to Rae1•Nup98. We localized this competing activity of M to its finger using a synthetic peptide. Collectively, our data suggest that Rae1 serves as a binding protein for the phosphate backbone of any nucleic acid and that the finger of M mimics this ligand. In the context of mRNA export, we propose that a given mRNA segment, after having been deproteinated by helicase, is transiently reproteinated by Nup98-tethered Rae1. We suggest that such repetitive cycles provide cytoplasmic stopover sites required for ratcheting mRNA across the nuclear pore.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
mRNA export factor
A
339Homo sapiensMutation(s): 0 
Gene Names: RAE1 (MRNP41)
Find proteins for P78406 (Homo sapiens)
Go to Gene View: RAE1
Go to UniProtKB:  P78406
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear pore complex protein Nup98-Nup96
B
59Homo sapiensMutation(s): 0 
Gene Names: NUP98 (ADAR2)
EC: 3.4.21.-
Find proteins for P52948 (Homo sapiens)
Go to Gene View: NUP98
Go to UniProtKB:  P52948
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Matrix protein
C
188Vesicular stomatitis Indiana virus (strain 85CLB South America)Mutation(s): 0 
Gene Names: M
Find proteins for Q8B0H7 (Vesicular stomatitis Indiana virus (strain 85CLB South America))
Go to UniProtKB:  Q8B0H7
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.213 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 141.372α = 90.00
b = 141.372β = 90.00
c = 78.462γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical InstituteUnited States--

Revision History 

  • Version 1.0: 2014-06-25
    Type: Initial release
  • Version 1.1: 2014-10-01
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy
  • Version 1.3: 2018-03-21
    Type: Data collection