5LGP

Crystal structure of mouse CARM1 in complex with ligand P1C3s


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Transition state mimics are valuable mechanistic probes for structural studies with the arginine methyltransferase CARM1.

van Haren, M.J.Marechal, N.Troffer-Charlier, N.Cianciulli, A.Sbardella, G.Cavarelli, J.Martin, N.I.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: 3625-3630

  • DOI: 10.1073/pnas.1618401114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Coactivator associated arginine methyltransferase 1 (CARM1) is a member of the protein arginine methyltransferase (PRMT) family and methylates a range of proteins in eukaryotic cells. Overexpression of CARM1 is implicated in a number of cancers, and ...

    Coactivator associated arginine methyltransferase 1 (CARM1) is a member of the protein arginine methyltransferase (PRMT) family and methylates a range of proteins in eukaryotic cells. Overexpression of CARM1 is implicated in a number of cancers, and it is therefore seen as a potential therapeutic target. Peptide sequences derived from the well-defined CARM1 substrate poly(A)-binding protein 1 (PABP1) were covalently linked to an adenosine moiety as in the AdoMet cofactor to generate transition state mimics. These constructs were found to be potent CARM1 inhibitors and also formed stable complexes with the enzyme. High-resolution crystal structures of CARM1 in complex with these compounds confirm a mode of binding that is indeed reflective of the transition state at the CARM1 active site. Given the transient nature of PRMT-substrate complexes, such transition state mimics represent valuable chemical tools for structural studies aimed at deciphering the regulation of arginine methylation mediated by the family of arginine methyltransferases.


    Organizational Affiliation

    Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone-arginine methyltransferase CARM1
A, B, C, D
361Mus musculusMutation(s): 0 
Gene Names: Carm1 (Prmt4)
EC: 2.1.1.319
Find proteins for Q9WVG6 (Mus musculus)
Go to UniProtKB:  Q9WVG6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Polyadenylate-binding protein 1
E, F, G, H
13Homo sapiensMutation(s): 0 
Gene Names: PABPC1 (PAB1, PABP1, PABPC2)
Find proteins for P11940 (Homo sapiens)
Go to Gene View: PABPC1
Go to UniProtKB:  P11940
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8ZB
Query on 8ZB

Download SDF File 
Download CCD File 
E, F, G, H
(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-propyl-oxolane-3,4-diol
C12 H17 N5 O3
BKDAOQOLDUJANJ-WOUKDFQISA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
LPD
Query on LPD

Download SDF File 
Download CCD File 
E, F, G, H
L-PROLINAMIDE
C5 H10 N2 O
VLJNHYLEOZPXFW-BYPYZUCNSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
E, F, G, H
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 74.794α = 90.00
b = 98.714β = 90.00
c = 207.253γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
PHENIXrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-04-05
    Type: Non-polymer description
  • Version 1.2: 2017-04-12
    Type: Database references