4HC4 | pdb_00004hc4

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 
    0.220 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

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 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.

Macromolecule Content 

  • Total Structure Weight: 42.61 kDa 
  • Atom Count: 2,904 
  • Modeled Residue Count: 326 
  • Deposited Residue Count: 376 
  • Unique protein chains: 1

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein arginine N-methyltransferase 6376Homo sapiensMutation(s): 1 
Gene Names: PRMT6HRMT1L6
EC: 2.1.1 (PDB Primary Data), 2.1.1.125 (PDB Primary Data), 2.1.1.319 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96LA8 (Homo sapiens)
Explore Q96LA8 
Go to UniProtKB:  Q96LA8
PHAROS:  Q96LA8
GTEx:  ENSG00000198890 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96LA8
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free:  0.220 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
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
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

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
  • Version 1.3: 2024-10-30
    Changes: Data collection, Structure summary