Human HMT1 hnRNP methyltransferase-like protein 6 (S. cerevisiae)

Experimental Data Snapshot

  • Resolution: 1.97 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 

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Structural basis of arginine asymmetrical dimethylation by PRMT6.

Wu, H.Zheng, W.Eram, M.S.Vhuiyan, M.Dong, A.Zeng, H.He, H.Brown, P.Frankel, A.Vedadi, M.Luo, M.Min, J.

(2016) Biochem J 473: 3049-3063

  • DOI: https://doi.org/10.1042/BCJ20160537
  • Primary Citation of Related Structures:  
    4HC4, 4QQK, 5HZM

  • PubMed Abstract: 

    PRMT6 is a type I protein arginine methyltransferase, generating the asymmetric dimethylarginine mark on proteins such as histone H3R2. Asymmetric dimethylation of histone H3R2 by PRMT6 acts as a repressive mark that antagonizes trimethylation of H3 lysine 4 by the MLL histone H3K4 methyltransferase. PRMT6 is overexpressed in several cancer types, including prostate, bladder and lung cancers; therefore, it is of great interest to develop potent and selective inhibitors for PRMT6. Here, we report the synthesis of a potent bisubstrate inhibitor GMS [6'-methyleneamine sinefungin, an analog of sinefungin (SNF)], and the crystal structures of human PRMT6 in complex, respectively, with S-adenosyl-L-homocysteine (SAH) and the bisubstrate inhibitor GMS that shed light on the significantly improved inhibition effect of GMS on methylation activity of PRMT6 compared with SAH and an S-adenosyl-L-methionine competitive methyltransferase inhibitor SNF. In addition, we also crystallized PRMT6 in complex with SAH and a short arginine-containing peptide. Based on the structural information here and available in the PDB database, we proposed a mechanism that can rationalize the distinctive arginine methylation product specificity of different types of arginine methyltransferases and pinpoint the structural determinant of such a specificity.

  • Organizational Affiliation

    Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5J 1L7, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein arginine N-methyltransferase 6376Homo sapiensMutation(s): 1 
Gene Names: PRMT6HRMT1L6
EC: 2.1.1 (PDB Primary Data), (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96LA8 (Homo sapiens)
Explore Q96LA8 
Go to UniProtKB:  Q96LA8
GTEx:  ENSG00000198890 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96LA8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.97 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.981α = 90
b = 93.981β = 90
c = 108.878γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-17
    Type: Initial release
  • Version 1.1: 2018-05-16
    Changes: Data collection, Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description