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: 2.84 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

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
  • Primary Citation of Related Structures:  
    5FIR

  • 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 an XTBD-XRN2 complex ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
5'-3' EXORIBONUCLEASE 2 HOMOLOG
A, C, E, G, I, K
A, C, E, G, I, K
636Caenorhabditis elegansMutation(s): 0 
Gene Names: xrn-2Y48B6A.3
EC: 3.1.13
UniProt
Find proteins for Q9U299 (Caenorhabditis elegans)
Explore Q9U299 
Go to UniProtKB:  Q9U299
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9U299
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PAXT-1
B, D, F, H, J, L
B, D, F, H, J, L
78Caenorhabditis elegansMutation(s): 0 
Gene Names: paxt-1CELE_R05D11.6R05D11.6
UniProt
Find proteins for Q21738 (Caenorhabditis elegans)
Explore Q21738 
Go to UniProtKB:  Q21738
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ21738
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth E],
BA [auth E],
CA [auth G],
DA [auth G],
EA [auth G],
AA [auth E],
BA [auth E],
CA [auth G],
DA [auth G],
EA [auth G],
FA [auth G],
GA [auth I],
HA [auth I],
IA [auth I],
JA [auth K],
KA [auth K],
LA [auth K],
M [auth A],
MA [auth K],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth C],
V [auth C],
W [auth C],
X [auth E],
Y [auth E],
Z [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, C, E, G, I, K
A, C, E, G, I, K
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.21α = 90
b = 200.77β = 90
c = 202.99γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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