› 4nw3

X-ray diffraction
2.82Å resolution

Crystal structure of MLL CXXC domain in complex with a CpG DNA

Released:
DOI: 10.2210/pdb4nw3/pdb
PDB entry 4nw3 coloured by chain, front view.
PDB entry 4nw3 coloured by chain, side view.
PDB entry 4nw3 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants.
Xu C, Liu K, Lei M, Yang A, Li Y, Hughes TR, Min J
Structure 26 85-95.e3 (2018)
PMID: 29276034

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + a [histone H3]-L-lysine(4) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(4)
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117890 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
MLL cleavage product N320 Chain: A
Molecule details ›
Chain: A
Length: 76 amino acids
Theoretical weight: 8.81 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q03164 (Residues: 1147-1204; Coverage: 2%)
Gene names: ALL1, CXXC7, HRX, HTRX, KMT2A, MLL, MLL1, TRX1
Sequence domains: CXXC zinc finger domain
5'-D(*GP*CP*CP*AP*TP*CP*GP*AP*TP*GP*GP*C)-3' Chains: B, C
Molecule details ›
Chains: B, C
Length: 12 nucleotides
Theoretical weight: 3.66 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: C2
Unit cell:
a: 70.327Å b: 40.225Å c: 60.959Å
α: 90° β: 93.51° γ: 90°
R-values:
R R work R free
0.221 0.218 0.266
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

9 review citations

Understanding the interplay between CpG island-associated gene promoters and H3K4 methylation.
Hughes et al. (2020)
8 more

3 mentions without citation

Detecting and interpreting DNA methylation marks.
Ren et al. (2018)
2 more