› 6bw3

X-ray diffraction
2.2Å resolution

Crystal structure of RBBP4 in complex with PRDM3 N-terminal peptide

Released:
DOI: 10.2210/pdb6bw3/pdb
PDB entry 6bw3 coloured by chain, front view.
PDB entry 6bw3 coloured by chain, side view.
PDB entry 6bw3 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Direct interaction between the PRDM3 and PRDM16 tumor suppressors and the NuRD chromatin remodeling complex.
Ivanochko D, Halabelian L, Henderson E, Savitsky P, Jain H, Marcon E, Duan S, Hutchinson A, Seitova A, Barsyte-Lovejoy D, Filippakopoulos P, Greenblatt J, Lima-Fernandes E, Arrowsmith CH
Nucleic Acids Res 47 1225-1238 (2019)
PMID: 30462309

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + a [histone H3]-L-lysine(9) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(9)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-169830 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Histone-binding protein RBBP4 Chains: A, C
Molecule details ›
Chains: A, C
Length: 427 amino acids
Theoretical weight: 47.85 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q09028 (Residues: 1-425; Coverage: 100%)
Gene names: RBAP48, RBBP4
Sequence domains:
Structure domains: YVTN repeat-like/Quinoprotein amine dehydrogenase
Histone-lysine N-methyltransferase MECOM Chains: B, D
Molecule details ›
Chains: B, D
Length: 12 amino acids
Theoretical weight: 1.38 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q03112 (Residues: 1-12; Coverage: 1%)
Gene names: EVI1, MDS1, MECOM, PRDM3

Ligands and Environments

1 bound ligand:
Ligand UNX 12 x UNX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E SUPERBRIGHT
Spacegroup: P21
Unit cell:
a: 75.979Å b: 59.822Å c: 101.773Å
α: 90° β: 94.55° γ: 90°
R-values:
R R work R free
0.217 0.215 0.246
Expression systems:
  • Spodoptera frugiperda
  • Not provided

Quick links

Citations

5 review citations

Multifaceted Role of PRDM Proteins in Human Cancer.
Casamassimi et al. (2020)
4 more

1 mention without citation

Direct interaction between the PRDM3 and PRDM16 tumor suppressors and the NuRD chromatin remodeling complex.
Ivanochko et al. (2019)