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 
  • R-Value Observed: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.4 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 U S A 111: 9127-9132

  • DOI: 10.1073/pnas.1409076111
  • Structures With Same Primary Citation

  • 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 blobel@rockefeller.edu yren@rockefeller.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
mRNA export factor
A
339Homo sapiensMutation(s): 0 
Gene Names: RAE1MRNP41
Find proteins for P78406 (Homo sapiens)
Go to UniProtKB:  P78406
NIH Common Fund Data Resources
PHAROS  P78406
Protein Feature View
  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear pore complex protein Nup98-Nup96
B
59Homo sapiensMutation(s): 0 
Gene Names: NUP98ADAR2
EC: 3.4.21
Find proteins for P52948 (Homo sapiens)
Go to UniProtKB:  P52948
NIH Common Fund Data Resources
PHAROS  P52948
Protein Feature View
  • Reference Sequence

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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
Protein Feature View
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.217 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.372α = 90
b = 141.372β = 90
c = 78.462γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History 

  • Version 1.0: 2014-06-25
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy
  • Version 1.3: 2018-03-21
    Changes: Data collection
  • Version 1.4: 2019-11-20
    Changes: Author supporting evidence