5YD0

Crystal structure of Schlafen 13 (SLFN13) N'-domain

  • Classification: HYDROLASE
  • Organism(s): Rattus norvegicus
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2017-09-09 Released: 2018-03-28 
  • Deposition Author(s): Yang, J.-Y., Gao, S.
  • Funding Organization(s): National Natural Science Foundation of China, Ministry of Science and Technology (China), Natural Science Foundation of Guangdong Province

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.18 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of Schlafen13 reveals a new class of tRNA/rRNA- targeting RNase engaged in translational control

Yang, J.Y.Deng, X.Y.Li, Y.S.Ma, X.C.Feng, J.X.Yu, B.Chen, Y.Luo, Y.L.Wang, X.Chen, M.L.Fang, Z.X.Zheng, F.X.Li, Y.P.Zhong, Q.Kang, T.B.Song, L.B.Xu, R.H.Zeng, M.S.Chen, W.Zhang, H.Xie, W.Gao, S.

(2018) Nat Commun 9: 1165-1165

  • DOI: https://doi.org/10.1038/s41467-018-03544-x
  • Primary Citation of Related Structures:  
    5YD0

  • PubMed Abstract: 

    Cleavage of transfer (t)RNA and ribosomal (r)RNA are critical and conserved steps of translational control for cells to overcome varied environmental stresses. However, enzymes that are responsible for this event have not been fully identified in high eukaryotes. Here, we report a mammalian tRNA/rRNA-targeting endoribonuclease: SLFN13, a member of the Schlafen family. Structural study reveals a unique pseudo-dimeric U-pillow-shaped architecture of the SLFN13 N'-domain that may clamp base-paired RNAs. SLFN13 is able to digest tRNAs and rRNAs in vitro, and the endonucleolytic cleavage dissevers 11 nucleotides from the 3'-terminus of tRNA at the acceptor stem. The cytoplasmically localised SLFN13 inhibits protein synthesis in 293T cells. Moreover, SLFN13 restricts HIV replication in a nucleolytic activity-dependent manner. According to these observations, we term SLFN13 RNase S13. Our study provides insights into the modulation of translational machinery in high eukaryotes, and sheds light on the functional mechanisms of the Schlafen family.


  • Organizational Affiliation

    State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, Guangdong, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Schlafen 8
A, B, C, D
366Rattus norvegicusMutation(s): 0 
Gene Names: Slfn13Slfn8
UniProt
Find proteins for Q5U311 (Rattus norvegicus)
Explore Q5U311 
Go to UniProtKB:  Q5U311
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5U311
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.18 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.968α = 90
b = 134.065β = 105.55
c = 77.587γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina81772977, 31722016, 31470729
Ministry of Science and Technology (China)China2013CB910500
Natural Science Foundation of Guangdong ProvinceChina2014TQ01R584, 2014A030312015

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-28
    Type: Initial release
  • Version 1.1: 2018-04-11
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references