Crystal structure of human NSun6/tRNA/SAM

Experimental Data Snapshot

  • Resolution: 3.25 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

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Structural basis for substrate binding and catalytic mechanism of a human RNA:m5C methyltransferase NSun6

Liu, R.J.Long, T.Li, J.Li, H.Wang, E.D.

(2017) Nucleic Acids Res 45: 6684-6697

  • DOI: https://doi.org/10.1093/nar/gkx473
  • Primary Citation of Related Structures:  
    5WWQ, 5WWR, 5WWS, 5WWT

  • PubMed Abstract: 

    5-methylcytosine (m5C) modifications of RNA are ubiquitous in nature and play important roles in many biological processes such as protein translational regulation, RNA processing and stress response. Aberrant expressions of RNA:m5C methyltransferases are closely associated with various human diseases including cancers. However, no structural information for RNA-bound RNA:m5C methyltransferase was available until now, hindering elucidation of the catalytic mechanism behind RNA:m5C methylation. Here, we have solved the structures of NSun6, a human tRNA:m5C methyltransferase, in the apo form and in complex with a full-length tRNA substrate. These structures show a non-canonical conformation of the bound tRNA, rendering the base moiety of the target cytosine accessible to the enzyme for methylation. Further biochemical assays reveal the critical, but distinct, roles of two conserved cysteine residues for the RNA:m5C methylation. Collectively, for the first time, we have solved the complex structure of a RNA:m5C methyltransferase and addressed the catalytic mechanism of the RNA:m5C methyltransferase family, which may allow for structure-based drug design toward RNA:m5C methyltransferase-related diseases.

  • Organizational Affiliation

    State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, P. R. China.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Putative methyltransferase NSUN6C [auth A],
D [auth B]
477Homo sapiensMutation(s): 0 
Gene Names: NSUN6NOPD1
EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TEA1 (Homo sapiens)
Explore Q8TEA1 
Go to UniProtKB:  Q8TEA1
GTEx:  ENSG00000241058 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TEA1
Sequence Annotations
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
tRNAA [auth C],
B [auth D]
75Homo sapiens
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 3.25 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 205.236α = 90
b = 170.262β = 108.63
c = 76.883γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-3000data scaling
PDB_EXTRACTdata extraction
SCALEPACKdata reduction
HKLdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Data collection
  • Version 1.2: 2017-09-20
    Changes: Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description