Crystal structure of ribonuclease

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

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This is version 1.3 of the entry. See complete history


Structural basis for recognition of 2',5'-linked oligoadenylates by human ribonuclease L

Tanaka, N.Nakanishi, M.Kusakabe, Y.Goto, Y.Kitade, Y.Nakamura, K.T.

(2004) EMBO J 23: 3929-3938

  • DOI: https://doi.org/10.1038/sj.emboj.7600420
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    An interferon-induced endoribonuclease, ribonuclease L (RNase L), is implicated in both the molecular mechanism of action of interferon and the fundamental control of RNA stability in mammalian cells. RNase L is catalytically active only after binding to an unusual activator molecule containing a 5'-phosphorylated 2',5'-linked oligoadenylate (2-5A), in the N-terminal half. Here, we report the crystal structure of the N-terminal ankyrin repeat domain (ANK) of human RNase L complexed with the activator 2-5A. This is the first structural view of an ankyrin repeat structure directly interacting with a nucleic acid, rather than with a protein. The ANK domain folds into eight ankyrin repeat elements and forms an extended curved structure with a concave surface. The 2-5A molecule is accommodated at a concave site and directly interacts with ankyrin repeats 2-4. Interestingly, two structurally equivalent 2-5A binding motifs are found at repeats 2 and 4. The structural basis for 2-5A recognition by ANK is essential for designing stable 2-5As with a high likelihood of activating RNase L.

  • Organizational Affiliation

    School of Pharmaceutical Sciences, Showa University, Hatanodai, Shinagawa-ku, Tokyo, Japan. ntanaka@pharm.showa-u.ac.jp

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-5A-dependent ribonuclease285Homo sapiensMutation(s): 1 
EC: 3.1.26
UniProt & NIH Common Fund Data Resources
Find proteins for Q05823 (Homo sapiens)
Explore Q05823 
Go to UniProtKB:  Q05823
GTEx:  ENSG00000135828 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05823
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 25A

Download Ideal Coordinates CCD File 
C30 H38 N15 O19 P3
Binding Affinity Annotations 
IDSourceBinding Affinity
25A BindingDB:  1WDY IC50: min: 1.1, max: 20 (nM) from 3 assay(s)
EC50: 0.21 (nM) from 1 assay(s)
PDBBind:  1WDY IC50: 13 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.203α = 90
b = 72.834β = 90
c = 82.634γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-10-05
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations