5FIR | pdb_00005fir

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 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.4 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: https://doi.org/10.1038/nsmb.3155
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 505.98 kDa 
  • Atom Count: 33,550 
  • Modeled Residue Count: 4,073 
  • Deposited Residue Count: 4,284 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
5'-3' EXORIBONUCLEASE 2 HOMOLOG
A, C, E, G, I
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
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
PAXT-1
B, D, F, H, J
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
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / 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
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, C, E, G, I
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 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
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
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary