1YYO

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


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 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease IIIE [auth A],
F [auth B]
221Aquifex aeolicusMutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67082
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
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]
12N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download Ideal Coordinates CCD File 
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 = 84.486α = 90
b = 61.625β = 90
c = 131.114γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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