5FIR

Crystal structure of C. elegans XRN2 in complex with the XRN2-binding domain of PAXT-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.836 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis and Function of Xrn2-Binding by Xtb Domains

Richter, H.Katic, I.Gut, H.Grosshans, H.

(2016) Nat.Struct.Mol.Biol. 23: 164

  • DOI: 10.1038/nsmb.3155

  • PubMed Abstract: 
  • The RNase XRN2 is essential in RNA metabolism. In Caenorhabditis elegans, XRN2 functions with PAXT-1, which shares a putative XRN2-binding domain (XTBD) with otherwise unrelated mammalian proteins. Here, we characterize the structure and function of ...

    The RNase XRN2 is essential in RNA metabolism. In Caenorhabditis elegans, XRN2 functions with PAXT-1, which shares a putative XRN2-binding domain (XTBD) with otherwise unrelated mammalian proteins. Here, we characterize the structure and function of an XTBD-XRN2 complex. Although XTBD stably interconnects two XRN2 domains through numerous interacting residues, mutation of a single critical residue suffices to disrupt XTBD-XRN2 complexes in vitro and to recapitulate paxt-1-null mutant phenotypes in vivo. Demonstrating conservation of function, vertebrate XTBD-containing proteins bind XRN2 in vitro, and human CDKN2AIPNL (HsC2AIL) can substitute for PAXT-1 in vivo. In vertebrates, which express three distinct XTBD-containing proteins, XRN2 may partition into distinct stable heterodimeric complexes, which probably differ in subcellular localization or function. In C. elegans, complex formation with PAXT-1, the sole XTBD protein, serves to preserve the stability of XRN2 in the absence of substrate.


    Organizational Affiliation

    Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5'-3' EXORIBONUCLEASE 2 HOMOLOG
A, C, E, G, I, K
636Caenorhabditis elegansGene Names: xrn-2
EC: 3.1.13.-
Find proteins for Q9U299 (Caenorhabditis elegans)
Go to UniProtKB:  Q9U299
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PAXT-1
B, D, F, H, J, L
78Caenorhabditis elegansGene Names: paxt-1
Find proteins for Q21738 (Caenorhabditis elegans)
Go to UniProtKB:  Q21738
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, C, E, G, I, K
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F, G, H, I, J, K, L
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.836 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 170.210α = 90.00
b = 200.770β = 90.00
c = 202.990γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-01-20
    Type: Initial release
  • Version 1.1: 2016-01-27
    Type: Database references
  • Version 1.2: 2016-03-02
    Type: Database references