Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42.6 kDa 
• Atom Count: 2,788 
• Modelled Residue Count: 324 
• Deposited Residue Count: 376 
• Unique protein chains: 1

 4QQK

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

• PDB DOI: 10.2210/pdb4QQK/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2014-06-27 Released: 2014-07-16 
• Deposition Author(s): Dong, A., Zeng, H., He, H., Wernimont, A., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Brown, P.J., Min, J., Luo, M., Wu, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.207 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 

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

• PubMed: 27480107 
• DOI: 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.

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Organizational Affiliation: 

Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5J 1L7, Canada Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein arginine N-methyltransferase 6	A	376	Homo sapiens	Mutation(s): 1  Gene Names: PRMT6, HRMT1L6 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
37H	B [auth A]	(5S)-5-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}-N~6~-carbamimidoyl-L-lysine C17 H27 N9 O5 PRQKNHVENSAKGM-TVDBPQCTSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
UNX	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.207 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 
• Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.211	α = 90
b = 95.211	β = 90
c = 108.359	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-16 
Deposition Author(s): Dong, A., Zeng, H., He, H., Wernimont, A., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Brown, P.J., Min, J., Luo, M., Wu, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2014-07-16
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Structure summary
• Version 1.2: 2018-05-16
  Changes: Data collection, Database references