5WWS

Crystal structure of human NSun6/tRNA/SAM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.247 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1093/nar/gkx473
  • Primary Citation of Related Structures:  5WWQ, 5WWR, 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 methyltransferase ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Putative methyltransferase NSUN6
A, B
477Homo sapiensGene Names: NSUN6 (NOPD1)
EC: 2.1.1.-
Find proteins for Q8TEA1 (Homo sapiens)
Go to Gene View: NSUN6
Go to UniProtKB:  Q8TEA1
Entity ID: 1
MoleculeChainsLengthOrganism
tRNAC,D75Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download SDF File 
Download CCD File 
A, B
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.247 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.193 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 205.236α = 90.00
b = 170.262β = 108.63
c = 76.883γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data scaling
SCALEPACKdata scaling
PHASERphasing
HKL-3000data collection
HKLdata reduction
SCALEPACKdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-08-30
    Type: Data collection
  • Version 1.2: 2017-09-20
    Type: Database references