Crystal structure of swt1 C-terminal domain from yeast

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 

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This is version 1.3 of the entry. See complete history


High-resolution crystal structure reveals a HEPN domain at the C-terminal region of S. cerevisiae RNA endonuclease Swt1.

Peng, S.Zhou, K.Wang, W.Gao, Z.Dong, Y.Liu, Q.

(2014) Biochem Biophys Res Commun 453: 826-832

  • DOI: https://doi.org/10.1016/j.bbrc.2014.10.040
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Swt1 is an RNA endonuclease that plays an important role in quality control of nuclear messenger ribonucleoprotein particles (mRNPs) in eukaryotes; however, its structural details remain to be elucidated. Here, we report the crystal structure of the C-terminal (CT) domain of Swt1 from Saccharomyces cerevisiae, which shares common characteristics of higher eukaryotes and prokaryotes nucleotide binding (HEPN) domain superfamily. To study in detail the full-length protein structure, we analyzed the low-resolution architecture of Swt1 in solution using small angle X-ray scattering (SAXS) method. Both the CT domain and middle domain exhibited a good fit upon superimposing onto the molecular envelope of Swt1. Our study provides the necessary structural information for detailed analysis of the functional role of Swt1, and its importance in the process of nuclear mRNP surveillance.

  • Organizational Affiliation

    Multidisciplinary Research Center, Institute for High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China. Electronic address: pengsx@ihep.ac.cn.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional protein SWT1167Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SWT1YOR166CO3595
Find proteins for Q12104 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12104 
Go to UniProtKB:  Q12104
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12104
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.518α = 90
b = 61.518β = 90
c = 84.967γ = 120
Software Package:
Software NamePurpose
MAR345data collection
HKL-2000data reduction
SCALEPACKdata 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: 2014-12-24
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2024-04-03
    Changes: Data collection, Database references, Refinement description