1WDY

Crystal structure of ribonuclease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 10.1038/sj.emboj.7600420
  • Primary Citation of Related Structures:  
    1WDY

  • 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 bindin ...

    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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2-5A-dependent ribonucleaseA285Homo sapiensMutation(s): 1 
Gene Names: RNASELRNS4
EC: 3.1.26
Find proteins for Q05823 (Homo sapiens)
Explore Q05823 
Go to UniProtKB:  Q05823
NIH Common Fund Data Resources
PHAROS  Q05823
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
25A
Query on 25A

Download CCD File 
A
5'-O-MONOPHOSPHORYLADENYLYL(2'->5')ADENYLYL(2'->5')ADENOSINE
C30 H38 N15 O19 P3
SIIZPVYVXNXXQG-UQTMIEBXSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
25AIC50 :  13   nM  PDBBind
25AIC50:  20   nM  BindingDB
25AEC50:  0.20999999344348907   nM  BindingDB
25AIC50:  1.100000023841858   nM  BindingDB
25AIC50:  13   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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