› 5dxa

X-ray diffraction
2.07Å resolution

Crystal structure of CARM1, sinefungin, and methylated PABP1 peptide (R460)

Released:
DOI: 10.2210/pdb5dxa/pdb
PDB entry 5dxa coloured by chain, front view.
PDB entry 5dxa coloured by chain, side view.
PDB entry 5dxa coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural Insights into Ternary Complex Formation of Human CARM1 with Various Substrates.
Boriack-Sjodin PA, Jin L, Jacques SL, Drew A, Sneeringer C, Scott MP, Moyer MP, Ribich S, Moradei O, Copeland RA
ACS Chem Biol 11 763-71 (2016)
PMID: 26551522

Function and Biology Details

Reaction catalysed: 
(1a) S-adenosyl-L-methionine + [protein]-L-arginine = S-adenosyl-L-homocysteine + [protein]-N(omega)-methyl-L-arginine
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero tetramer
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-145994 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Histone-arginine methyltransferase CARM1 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 349 amino acids
Theoretical weight: 39.62 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q86X55 (Residues: 134-479; Coverage: 57%)
Gene names: CARM1, PRMT4
Sequence domains: Ribosomal protein L11 methyltransferase (PrmA)
Structure domains:
Polyadenylate-binding protein 1 Chains: F, G, I
Molecule details ›
Chains: F, G, I
Length: 19 amino acids
Theoretical weight: 1.95 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P11940 (Residues: 449-466; Coverage: 3%)
Gene names: PAB1, PABP, PABP1, PABPC1, PABPC2

Ligands and Environments

2 bound ligands:
Ligand SFG 4 x SFG
Ligand GOL 3 x GOL
2 modified residues:
Ligand DA2 3 x DA2
Ligand NMM 3 x NMM

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P21212
Unit cell:
a: 75.179Å b: 98.693Å c: 207.483Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.198 0.244
Expression systems:
  • Spodoptera frugiperda
  • Not provided

Quick links

Citations

5 review citations

Protein arginine methylation: from enigmatic functions to therapeutic targeting.
Wu et al. (2021)
4 more

2 mentions without citation

Deep Neural Network Classifier for Virtual Screening Inhibitors of (S)-Adenosyl-L-Methionine (SAM)-Dependent Methyltransferase Family.
Li et al. (2019)
1 more