Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 38.97 kDa 
• Atom Count: 2,930 
• Modelled Residue Count: 260 
• Deposited Residue Count: 260 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

 1RC7

Crystal structure of RNase III Mutant E110K from Aquifex Aeolicus complexed with ds-RNA at 2.15 Angstrom Resolution

• PDB DOI: 10.2210/pdb1RC7/pdb
• NDB: PR0107

• Classification: HYDROLASE/RNA
• Organism(s): Aquifex aeolicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2003-11-03 Released: 2004-03-30 
• Deposition Author(s): Blaszczyk, J., Gan, J., Ji, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.242 
• R-Value Work: 0.192 
• R-Value Observed: 0.192 

Literature

Noncatalytic Assembly of Ribonuclease III with Double-Stranded RNA.

Blaszczyk, J., Gan, J., Tropea, J.E., Court, D.L., Waugh, D.S., Ji, X.

(2004) Structure 12: 457-466

• PubMed: 15016361 
• DOI: 10.1016/j.str.2004.02.004
• Primary Citation of Related Structures:  
  1RC5, 1RC7


• PubMed Abstract: 
  

Ribonuclease III (RNase III) represents a family of double-stranded RNA (dsRNA) endonucleases. The simplest bacterial enzyme contains an endonuclease domain (endoND) and a dsRNA binding domain (dsRBD). RNase III can affect RNA structure and gene expression in either of two ways: as a dsRNA-processing enzyme that cleaves dsRNA, or as a dsRNA binding protein that binds but does not cleave dsRNA. We previously determined the endoND structure of Aquifex aeolicus RNase III (Aa-RNase III) and modeled a catalytic complex of full-length Aa-RNase III with dsRNA. Here, we present the crystal structure of Aa-RNase III in complex with dsRNA, revealing a noncatalytic assembly. The major differences between the two functional forms of RNase III.dsRNA are the conformation of the protein and the orientation and location of dsRNA. The flexibility of a 7 residue linker between the endoND and dsRBD enables the transition between these two forms.

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Related Citations: 

• Crystallographic and Modelling Studies of RNase III Suggest a Mechanism for Double-Stranded RNA Cleavage
  Blaszczyk, J., Tropea, J.E., Bubunenko, M., Routzahn, K.M., Waugh, D.S., Court, D.L., Ji, X.
  (2001) Structure 9: 1225

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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	E [auth A]	220	Aquifex aeolicus	Mutation(s): 1  Gene Names: rnc, aq_946 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
5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3'	A [auth B], B [auth C], C [auth D], D [auth E]	10	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	F [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.242 
• R-Value Work: 0.192 
• R-Value Observed: 0.192 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.286	α = 90
b = 118.142	β = 90
c = 106.665	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-03-30 
Deposition Author(s): Blaszczyk, J., Gan, J., Ji, X.

Revision History  

• Version 1.0: 2004-03-30
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations