1ORI

Structure of the predominant protein arginine methyltransferase PRMT1

• PDB DOI: https://doi.org/10.2210/pdb1ORI/pdb

• Classification: TRANSFERASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-03-13 Released: 2003-05-27 
• Deposition Author(s): Zhang, X., Cheng, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.263 
• R-Value Work: 0.199 

Starting Model: experimental

Literature

Structure of the Predominant Protein Arginine Methyltransferase PRMT1 and Analysis of its Binding to Substrate Peptides

Zhang, X., Cheng, X.

(2003) Structure 11: 509-520

• PubMed: 12737817 
• DOI: https://doi.org/10.1016/s0969-2126(03)00071-6
• Primary Citation of Related Structures:  
  1OR8, 1ORH, 1ORI


• PubMed Abstract: 
  

  PRMT1 is the predominant type I protein arginine methyltransferase in mammals and highly conserved among all eukaryotes. It is essential for early postimplantation development in mouse. Here we describe the crystal structure of rat PRMT1 in complex with the reaction product AdoHcy and a 19 residue substrate peptide containing three arginines. The results reveal a two-domain structure-an AdoMet binding domain and a barrel-like domain-with the active site pocket located between the two domains. Mutagenesis studies confirmed that two active site glutamates are essential for enzymatic activity, and that dimerization of PRMT1 is essential for AdoMet binding. Three peptide binding channels are identified: two are between the two domains, and the third is on the surface perpendicular to the strands forming the beta barrel.

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Organizational Affiliation: 

Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 40.01 kDa 
• Atom Count: 2,703 
• Modelled Residue Count: 316 
• Deposited Residue Count: 343 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein arginine N-methyltransferase 1	A	343	Rattus norvegicus	Mutation(s): 0  Gene Names: HRMT1L2 OR PRMT1 EC: 2.1.1.125 (PDB Primary Data), 2.1.1.319 (UniProt)
UniProt
Find proteins for Q63009 (Rattus norvegicus) Explore Q63009  Go to UniProtKB:  Q63009

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	B [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
UNL	C [auth A], D [auth A]	Unknown ligand ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SAH	BindingDB:  1ORI	Ki: 400 (nM) from 1 assay(s)
		IC50: min: 250, max: 550 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.263 
• R-Value Work: 0.199 
• Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.27	α = 90
b = 88.27	β = 90
c = 145.14	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-05-27 
Deposition Author(s): Zhang, X., Cheng, X.

Revision History  

• Version 1.0: 2003-05-27
  Type: Initial release
  
• Version 1.1: 2008-04-02
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description