2NUG

Crystal structure of RNase III from Aquifex aeolicus complexed with ds-RNA at 1.7-Angstrom Resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

A stepwise model for double-stranded RNA processing by ribonuclease III.

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

(2007) Mol Microbiol 67: 143-154

  • DOI: 10.1111/j.1365-2958.2007.06032.x
  • Primary Citation of Related Structures:  
    2NUE, 2NUF, 2NUG

  • PubMed Abstract: 

    • RNA interference is mediated by small interfering RNAs produced by members of the ribonuclease III (RNase III) family represented by bacterial RNase III and eukaryotic Rnt1p, Drosha and Dicer. For mechanistic studies, bacterial RNase III has been a valuable model system for the family ...

    RNA interference is mediated by small interfering RNAs produced by members of the ribonuclease III (RNase III) family represented by bacterial RNase III and eukaryotic Rnt1p, Drosha and Dicer. For mechanistic studies, bacterial RNase III has been a valuable model system for the family. Previously, we have shown that RNase III uses two catalytic sites to create the 2-nucleotide (nt) 3' overhangs in its products. Here, we present three crystal structures of RNase III in complex with double-stranded RNA, demonstrating how Mg(2+) is essential for the formation of a catalytically competent protein-RNA complex, how the use of two Mg(2+) ions can drive the hydrolysis of each phosphodiester bond, and how conformational changes in both the substrate and the protein are critical elements for assembling the catalytic complex. Moreover, we have modelled a protein-substrate complex and a protein-reaction intermediate (transition state) complex on the basis of the crystal structures. Together, the crystal structures and the models suggest a stepwise mechanism for RNase III to execute the phosphoryl transfer reaction.

    Organizational Affiliation: 

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



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease IIIE [auth A],
F [auth B]		221Aquifex aeolicusMutation(s): 0 
Gene Names: rnc
EC: 3.1.26.3
UniProt
Find proteins for O67082 (Aquifex aeolicus (strain VF5))
Explore O67082 
Go to UniProtKB:  O67082
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67082
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-R(P*AP*AP*GP*GP*UP*CP*AP*UP*UP*CP*G)-3'A [auth C],
C [auth D]		11N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-R(P*AP*GP*UP*GP*GP*CP*CP*UP*UP*GP*C)-3'B [auth E],
D [auth F]		11N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download Ideal Coordinates CCD File 
G [auth C],
H [auth C],
I [auth E],
J [auth D],
K [auth D],
G [auth C],
H [auth C],
I [auth E],
J [auth D],
K [auth D],
L [auth F],
M [auth F],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.4α = 90
b = 119.9β = 90
c = 58.9γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-18
    Changes: Refinement description