1YYO | pdb_00001yyo

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 (Depositor), 0.283 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1YYO

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 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.

Macromolecule Content 

  • Total Structure Weight: 67.73 kDa 
  • Atom Count: 4,721 
  • Modeled Residue Count: 487 
  • Deposited Residue Count: 490 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
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
Find similar nucleic acids by:  Sequence
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 (Depositor), 0.283 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
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

View Full Validation Report



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