Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 32182.42 
• Atom Count: 2252 
• Residue Count: 285 
• Unique protein chains: 1

1WDY

Crystal structure of ribonuclease

• DOI: 10.2210/pdb1WDY/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 2004-05-19 Released: 2004-10-05 
• Deposition Author(s): Tanaka, N., Nakanishi, M., Kusakabe, Y., Goto, Y., Kitade, Y., Nakamura, K.T.

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Experimental Data Snapshot

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

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

• PubMed: 15385955 
• 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 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.

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Organizational Affiliation: 

School of Pharmaceutical Sciences, Showa University, Hatanodai, Shinagawa-ku, Tokyo, Japan. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
2-5A-dependent ribonuclease	A	285	Homo sapiens	Mutation(s): 1  Gene 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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
25A	A	5'-O-MONOPHOSPHORYLADENYLYL(2'->5')ADENYLYL(2'->5')ADENOSINE C30 H38 N15 O19 P3 SIIZPVYVXNXXQG-UQTMIEBXSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
25A	IC50: 1.1 - 20 nM (99) BINDINGDB
25A	EC50: 0.2 nM (99) BINDINGDB
25A	IC50: 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 = 63.203	α = 90.00
b = 72.834	β = 90.00
c = 82.634	γ = 90.00

Software Package:

Software Name	Purpose
MOSFLM	data reduction
REFMAC	refinement
AMoRE	phasing
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-05-19 
• Released Date: 2004-10-05 
• Deposition Author(s): Tanaka, N., Nakanishi, M., Kusakabe, Y., Goto, Y., Kitade, Y., Nakamura, K.T.

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