Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 70.30 kDa 
• Atom Count: 5136 
• Modelled Residue Count: 492 
• Deposited Residue Count: 498 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

2EZ6

Crystal structure of Aquifex aeolicus RNase III (D44N) complexed with product of double-stranded RNA processing

• PDB DOI: 10.2210/pdb2EZ6/pdb

• Classification: HYDROLASE/RNA
• Organism(s): Aquifex aeolicus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-11-10 Released: 2006-02-07 
• Deposition Author(s): Gan, J., Tropea, J.E., Austin, B.P., Court, D.L., Waugh, D.S., Ji, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.258 
• R-Value Work: 0.205 
• R-Value Observed: 0.205 

Literature

Structural Insight into the Mechanism of Double-Stranded RNA Processing by Ribonuclease III.

Gan, J., Tropea, J.E., Austin, B.P., Court, D.L., Waugh, D.S., Ji, X.

(2006) Cell 124: 355-366

• PubMed: 16439209 
• DOI: 10.1016/j.cell.2005.11.034
• Primary Citation of Related Structures:  
  2EZ6


• PubMed Abstract: 
  

Members of the ribonuclease III (RNase III) family are double-stranded RNA (dsRNA) specific endoribonucleases characterized by a signature motif in their active centers and a two-base 3' overhang in their products. While Dicer, which produces small interfering RNAs, is currently the focus of intense interest, the structurally simpler bacterial RNase III serves as a paradigm for the entire family. Here, we present the crystal structure of an RNase III-product complex, the first catalytic complex observed for the family. A 7 residue linker within the protein facilitates induced fit in protein-RNA recognition. A pattern of protein-RNA interactions, defined by four RNA binding motifs in RNase III and three protein-interacting boxes in dsRNA, is responsible for substrate specificity, while conserved amino acid residues and divalent cations are responsible for scissile-bond cleavage. The structure reveals a wealth of information about the mechanism of RNA hydrolysis that can be extrapolated to other RNase III family members.

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Organizational Affiliation: 

Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease III	C [auth A], D [auth B]	221	Aquifex aeolicus	Mutation(s): 1  Gene Names: rnc EC: 3.1.26.3
UniProt
Find proteins for O67082 (Aquifex aeolicus (strain VF5)) Explore O67082  Go to UniProtKB:  O67082

Entity ID: 1
Molecule	Chains	Length	Organism	Image
28-MER	A [auth C], B [auth D]	28	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	E [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.258 
• R-Value Work: 0.205 
• R-Value Observed: 0.205 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.839	α = 90
b = 50.976	β = 104.47
c = 113.746	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASES	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-11-10 
• Released Date: 2006-02-07 
Deposition Author(s): Gan, J., Tropea, J.E., Austin, B.P., Court, D.L., Waugh, D.S., Ji, X.

Revision History  

• Version 1.0: 2006-02-07
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations