Improved refinement of the Mtr4 apo crystal structure

Experimental Data Snapshot

  • Resolution: 3.39 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 

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This is version 1.2 of the entry. See complete history


The Mtr4 ratchet helix and arch domain both function to promote RNA unwinding.

Taylor, L.L.Jackson, R.N.Rexhepaj, M.King, A.K.Lott, L.K.van Hoof, A.Johnson, S.J.

(2014) Nucleic Acids Res 42: 13861-13872

  • DOI: https://doi.org/10.1093/nar/gku1208
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Mtr4 is a conserved Ski2-like RNA helicase and a subunit of the TRAMP complex that activates exosome-mediated 3'-5' turnover in nuclear RNA surveillance and processing pathways. Prominent features of the Mtr4 structure include a four-domain ring-like helicase core and a large arch domain that spans the core. The 'ratchet helix' is positioned to interact with RNA substrates as they move through the helicase. However, the contribution of the ratchet helix in Mtr4 activity is poorly understood. Here we show that strict conservation along the ratchet helix is particularly extensive for Ski2-like RNA helicases compared to related helicases. Mutation of residues along the ratchet helix alters in vitro activity in Mtr4 and TRAMP and causes slow growth phenotypes in vivo. We also identify a residue on the ratchet helix that influences Mtr4 affinity for polyadenylated substrates. Previous work indicated that deletion of the arch domain has minimal effect on Mtr4 unwinding activity. We now show that combining the arch deletion with ratchet helix mutations abolishes helicase activity and produces a lethal in vivo phenotype. These studies demonstrate that the ratchet helix modulates helicase activity and suggest that the arch domain plays a previously unrecognized role in unwinding substrates.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent RNA helicase DOB11,108Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: DOB1J1158MTR4MTR4/YJL050WYJL050W
Find proteins for P47047 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P47047 
Go to UniProtKB:  P47047
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47047
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.39 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.516α = 90
b = 133.516β = 90
c = 190.949γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2015-01-14
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations