4G8L

Active state of intact sensor domain of human RNase L with 2-5A bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Innate Immune Messenger 2-5A Tethers Human RNase L into Active High-Order Complexes.

Han, Y.Whitney, G.Donovan, J.Korennykh, A.

(2012) Cell Rep 2: 902-913

  • DOI: https://doi.org/10.1016/j.celrep.2012.09.004
  • Primary Citation of Related Structures:  
    4G8K, 4G8L

  • PubMed Abstract: 

    2',5'-linked oligoadenylates (2-5As) serve as conserved messengers of pathogen presence in the mammalian innate immune system. 2-5As induce self-association and activation of RNase L, which cleaves cytosolic RNA and promotes the production of interferons (IFNs) and cytokines driven by the transcription factors IRF-3 and NF-κB. We report that human RNase L is activated by forming high-order complexes, reminiscent of the mode of activation of the phylogenetically related transmembrane kinase/RNase Ire1 in the unfolded protein response. We describe crystal structures determined at 2.4 Å and 2.8 Å resolution, which show that two molecules of 2-5A at a time tether RNase L monomers via the ankyrin-repeat (ANK) domain. Each ANK domain harbors two distinct sites for 2-5A recognition that reside 50 Å apart. These data reveal a function for the ANK domain as a 2-5A-sensing homo-oligomerization device and describe a nonlinear, ultrasensitive regulation in the 2-5A/RNase L system poised for amplification of the IFN response.


  • Organizational Affiliation

    Department of Molecular Biology, Princeton University, 216 Schultz Laboratory, Princeton, NJ 08540, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-5A-dependent ribonuclease
A, B, C, D
337Homo sapiensMutation(s): 0 
Gene Names: RNASELRNS4
EC: 3.1.26
UniProt & NIH Common Fund Data Resources
Find proteins for Q05823 (Homo sapiens)
Explore Q05823 
Go to UniProtKB:  Q05823
PHAROS:  Q05823
GTEx:  ENSG00000135828 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05823
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
25A PDBBind:  4G8L Kd: 10 (nM) from 1 assay(s)
BindingDB:  4G8L IC50: min: 1.1, max: 20 (nM) from 3 assay(s)
EC50: 0.21 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.98α = 90
b = 164.11β = 100.2
c = 86.22γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-31
    Type: Initial release
  • Version 1.1: 2012-11-14
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description