1WDY

Crystal structure of ribonuclease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.202 

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

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2-5A-dependent ribonuclease
A
285Homo sapiensGene Names: RNASEL (RNS4)
EC: 3.1.26.-
Find proteins for Q05823 (Homo sapiens)
Go to Gene View: RNASEL
Go to UniProtKB:  Q05823
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
25A
Query on 25A

Download SDF File 
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: 1.1 - 20 nM (99) BINDINGDB
25AEC50: 0.2 nM (99) BINDINGDB
25AIC50: 13 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.203α = 90.00
b = 72.834β = 90.00
c = 82.634γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
AMoREphasing
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-10-05
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance