1YYO

Crystal structure of RNase III mutant E110K from Aquifex aeolicus complexed with double-stranded RNA at 2.9-Angstrom Resolution

• PDB DOI:  https://doi.org/10.2210/pdb1YYO/pdb
• NAKB: 1YYO

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


• Deposited: 2005-02-25 Released: 2005-11-22 
• 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: 2.90 Å
• R-Value Free: 0.292 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 

Literature

Intermediate states of ribonuclease III in complex with double-stranded RNA

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

(2005) Structure 13: 1435-1442

• PubMed: 16216575 
• DOI: https://doi.org/10.1016/j.str.2005.06.014
• Primary Citation of Related Structures:  
  1YYK, 1YYO, 1YYW, 1YZ9


• PubMed Abstract: 
  

Bacterial ribonuclease III (RNase III) can affect RNA structure and gene expression in either of two ways: as a processing enzyme that cleaves double-stranded (ds) RNA, or as a binding protein that binds but does not cleave dsRNA. We previously proposed a model of the catalytic complex of RNase III with dsRNA based on three crystal structures, including the endonuclease domain of RNase III with and without bound metal ions and a dsRNA binding protein complexed with dsRNA. We also reported a noncatalytic assembly observed in the crystal structure of an RNase III mutant, which binds but does not cleave dsRNA, complexed with dsRNA. We hypothesize that the RNase III*dsRNA complex can exist in two functional forms, a catalytic complex and a noncatalytic assembly, and that in between the two forms there may be intermediate states. Here, we present four crystal structures of RNase III complexed with dsRNA, representing possible intermediates.

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Organizational Affiliation: 

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

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: 67.73 kDa 
• Atom Count: 4,721 
• Modelled Residue Count: 487 
• Deposited Residue Count: 490 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease III	E [auth A], F [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
5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*G)-3'	A [auth C], B [auth D], C [auth E], D [auth F]	12	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	G [auth E]	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: 2.90 Å
• R-Value Free: 0.292 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.486	α = 90
b = 61.625	β = 90
c = 131.114	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-22 
Deposition Author(s): Gan, J., Tropea, J.E., Austin, B.P., Court, D.L., Waugh, D.S., Ji, X.

Revision History  

• Version 1.0: 2005-11-22
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Structure summary