Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 38.62 kDa 
• Atom Count: 2632 
• Modelled Residue Count: 299 
• Deposited Residue Count: 340 
• Unique protein chains: 1

3SMQ

Crystal structure of protein arginine methyltransferase 3

• PDB DOI: 10.2210/pdb3SMQ/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-06-28 Released: 2011-08-31 
• Deposition Author(s): Dobrovetsky, E., Dong, A., Walker, J.R., Siarheyeva, A., Senisterra, G., Wasney, G.A., Smil, D., Bolshan, Y., Nguyen, K.T., Allali-Hassani, A., Hajian, T., Poda, G., Bountra, C., Weigelt, J., Edwards, A.M., Al-Awar, R., Brown, P.J., Schapira, M., Arrowsmith, C.H., Vedadi, M., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.215 
• R-Value Work: 0.190 
• R-Value Observed: 0.191 

Literature

An allosteric inhibitor of protein arginine methyltransferase 3.

Siarheyeva, A., Senisterra, G., Allali-Hassani, A., Dong, A., Dobrovetsky, E., Wasney, G.A., Chau, I., Marcellus, R., Hajian, T., Liu, F., Korboukh, I., Smil, D., Bolshan, Y., Min, J., Wu, H., Zeng, H., Loppnau, P., Poda, G., Griffin, C., Aman, A., Brown, P.J., Jin, J., Al-Awar, R., Arrowsmith, C.H., Schapira, M., Vedadi, M.

(2012) Structure 20: 1425-1435

• PubMed: 22795084 
• DOI: 10.1016/j.str.2012.06.001
• Primary Citation of Related Structures:  
  3SMQ


• PubMed Abstract: 
  

PRMT3, a protein arginine methyltransferase, has been shown to influence ribosomal biosynthesis by catalyzing the dimethylation of the 40S ribosomal protein S2. Although PRMT3 has been reported to be a cytosolic protein, it has been shown to methylate histone H4 peptide (H4 1-24) in vitro. Here, we report the identification of a PRMT3 inhibitor (1-(benzo[d][1,2,3]thiadiazol-6-yl)-3-(2-cyclohexenylethyl)urea; compound 1) with IC50 value of 2.5 μM by screening a library of 16,000 compounds using H4 (1-24) peptide as a substrate. The crystal structure of PRMT3 in complex with compound 1 as well as kinetic analysis reveals an allosteric mechanism of inhibition. Mutating PRMT3 residues within the allosteric site or using compound 1 analogs that disrupt interactions with allosteric site residues both abrogated binding and inhibitory activity. These data demonstrate an allosteric mechanism for inhibition of protein arginine methyltransferases, an emerging class of therapeutic targets.

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Organizational Affiliation: 

Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS Centre, South Tower, Toronto, ON M5G 1L7, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein arginine N-methyltransferase 3	A	340	Homo sapiens	Mutation(s): 1  Gene Names: PRMT3, HRMT1L3 EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for O60678 (Homo sapiens) Explore O60678  Go to UniProtKB:  O60678
PHAROS:  O60678

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TDU	B [auth A]	1-(1,2,3-benzothiadiazol-6-yl)-3-[2-(cyclohex-1-en-1-yl)ethyl]urea C15 H18 N4 O S GGXCUZHEJUJACD-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
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]	UNKNOWN ATOM OR ION X

Binding Affinity Annotations
ID	Source	Binding Affinity
TDU	PDBBind:  3SMQ	Kd: 9500 (nM) from 1 assay(s)
	BindingDB:  3SMQ	Kd: 9500 (nM) from 1 assay(s)
		IC50: min: 1600, max: 2500 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.215 
• R-Value Work: 0.190 
• R-Value Observed: 0.191 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.649	α = 90
b = 70.649	β = 90
c = 171.977	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
Coot	model building
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-06-28 
• Released Date: 2011-08-31 
Deposition Author(s): Dobrovetsky, E., Dong, A., Walker, J.R., Siarheyeva, A., Senisterra, G., Wasney, G.A., Smil, D., Bolshan, Y., Nguyen, K.T., Allali-Hassani, A., Hajian, T., Poda, G., Bountra, C., Weigelt, J., Edwards, A.M., Al-Awar, R., Brown, P.J., Schapira, M., Arrowsmith, C.H., Vedadi, M., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2011-08-31
  Type: Initial release
  
• Version 1.1: 2013-07-24
  Changes: Database references