5DX0

Crystal structure of CARM1, sinefungin, and H3 peptide (R17)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Structural Insights into Ternary Complex Formation of Human CARM1 with Various Substrates.

Boriack-Sjodin, P.A., Jin, L., Jacques, S.L., Drew, A., Sneeringer, C., Scott, M.P., Moyer, M.P., Ribich, S., Moradei, O., Copeland, R.A.

(2016) Acs Chem.Biol. 11: 763-771

  • DOI: 10.1021/acschembio.5b00773
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Coactivator-associated arginine methyltransferase 1 (CARM1) is a protein arginine N-methyltransferase (PRMT) enzyme that has been implicated in a variety of cancers. CARM1 is known to methylate histone H3 and nonhistone substrates. To date, several c ...

    Coactivator-associated arginine methyltransferase 1 (CARM1) is a protein arginine N-methyltransferase (PRMT) enzyme that has been implicated in a variety of cancers. CARM1 is known to methylate histone H3 and nonhistone substrates. To date, several crystal structures of CARM1 have been solved, including structures with small molecule inhibitors, but no ternary structures with nucleoside and peptide substrates have been reported. Here, the crystal structures of human CARM1 with the S-adenosylmethione (SAM) mimic sinefungin and three different peptide sequences from histone H3 and PABP1 are presented, with both nonmethylated and singly methylated arginine residues exemplified. This is the first example of multiple substrate sequences solved in a single PRMT enzyme and demonstrates how the CARM1 binding site is capable of accommodating a variety of peptide sequences while maintaining a core binding mode for the unmethylated and monomethylated substrates. Comparison of these with other PRMT enzyme-peptide structures shows hydrogen bonding patterns that may be thematic of these binding sites.

    Organizational Affiliation: 

    Epizyme, Inc. 400 Technology Square, Cambridge, Massachusetts 02139, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone-arginine methyltransferase CARM1
A, B, C, D
349Homo sapiensMutation(s): 0 
Gene Names: CARM1 (PRMT4)
EC: 2.1.1.319
Find proteins for Q86X55 (Homo sapiens)
Go to Gene View: CARM1
Go to UniProtKB:  Q86X55
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
H3 peptide
F, G, H, I
20Homo sapiensMutation(s): 0 
Gene Names: H3F3A, H3F3B (H3.3A, H3F3, H3.3B)
Find proteins for P84243 (Homo sapiens)
Go to Gene View: H3F3A H3F3B
Go to UniProtKB:  P84243
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL
Download SDF File 
Download CCD File 
A, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
SFG
Query on SFG
Download SDF File 
Download CCD File 
A, B, C, D
SINEFUNGIN
ADENOSYL-ORNITHINE
C15 H23 N7 O5
LMXOHSDXUQEUSF-YECHIGJVSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
F, G, H, I
NON-POLYMERH2 N

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ACE
Query on ACE
F, G, H, I
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.211 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 75.722α = 90.00
b = 98.847β = 90.00
c = 208.670γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2015-09-23 
  • Released Date: 2015-11-25 
  • Deposition Author(s): Boriack-Sjodin, P.A.

Revision History 

  • Version 1.0: 2015-11-25
    Type: Initial release
  • Version 1.1: 2016-03-30
    Type: Database references