5T16

Crystal structure of yeast RNase III (Rnt1p) complexed with a non-hydrolyzable RNA substrate analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The Functional Cycle of Rnt1p: Five Consecutive Steps of Double-Stranded RNA Processing by a Eukaryotic RNase III.

Song, H.Fang, X.Jin, L.Shaw, G.X.Wang, Y.X.Ji, X.

(2017) Structure 25: 353-363

  • DOI: 10.1016/j.str.2016.12.013
  • Primary Citation of Related Structures:  
    5T16

  • PubMed Abstract: 
  • Double-stranded RNA (dsRNA)-specific RNase III proteins are required for RNA maturation and gene regulation. The mechanism of prokaryotic RNase IIIs has been well characterized, but how eukaryotic RNase IIIs (exemplified by Rnt1p, Drosha, and Dicer) work is less clear ...

    Double-stranded RNA (dsRNA)-specific RNase III proteins are required for RNA maturation and gene regulation. The mechanism of prokaryotic RNase IIIs has been well characterized, but how eukaryotic RNase IIIs (exemplified by Rnt1p, Drosha, and Dicer) work is less clear. Recently, we reported the crystal structure of Rnt1p in complex with RNA, revealing a double-ruler mechanism for substrate selection. Here, we present more structures of Rnt1p, either RNA free or RNA bound, featuring two major conformations of the enzyme. Using these structures with existing data, we describe the functional cycle of Rnt1p in five steps, selecting, loading, locking, cleavage, and releasing. We also describe atomic details of the two-Mg 2+ -ion catalytic mechanism that is applicable to all eukaryotic RNase III enzymes. Overall, our results indicate that substrate selection is achieved independent of cleavage, allowing the recognition of substrates with different structures while preserving the basic mechanism of cleavage.


    Related Citations: 
    • Structure of a eukaryotic RNase III postcleavage complex reveals a double-ruler mechanism for substrate selection.
      Liang, Y.H., Lavoie, M., Comeau, M.A., Abou Elela, S., Ji, X.
      (2014) Mol Cell 54: 431

    Organizational Affiliation

    Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA. Electronic address: jix@mail.nih.gov.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease 3 ABIJ276Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RNT1YMR239CYM9408.01CYM9959.21
EC: 3.1.26.3
Find proteins for Q02555 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02555 
Go to UniProtKB:  Q02555
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease 3 CDEFKLMN119Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RNT1YMR239CYM9408.01CYM9959.21
EC: 3.1.26.3
Find proteins for Q02555 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02555 
Go to UniProtKB:  Q02555
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
RNA substrate analogG, H, O, P34N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.037α = 90
b = 164.065β = 96.78
c = 176.855γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2016-08-18 
  • Released Date: 2017-02-08 
  • Deposition Author(s): Song, H., Ji, X.

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-08
    Type: Initial release
  • Version 1.1: 2017-02-15
    Changes: Database references