› 6ogk

X-ray diffraction
1.65Å resolution

MeCP2 MBD in complex with DNA

Released:
DOI: 10.2210/pdb6ogk/pdb
PDB entry 6ogk coloured by chain, front view.
PDB entry 6ogk coloured by chain, side view.
PDB entry 6ogk coloured by chain, top view.
Source organisms:
Primary publication:
Plasticity at the DNA recognition site of the MeCP2 mCG-binding domain.
Lei M, Tempel W, Chen S, Liu K, Min J
Biochim Biophys Acta Gene Regul Mech 1862 194409 (2019)
PMID: 31356990

Function and Biology Details

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-120393 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Methyl-CpG-binding protein 2 Chain: A
Molecule details ›
Chain: A
Length: 99 amino acids
Theoretical weight: 11.27 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P51608 (Residues: 77-167; Coverage: 19%)
Gene name: MECP2
Sequence domains: Methyl-CpG binding domain
Structure domains: Methyl-cpg-binding Protein 2; Chain A
DNA (5'-D(*GP*CP*CP*TP*AP*(5CM)P*AP*CP*TP*CP*CP*G)-3') Chain: D
Molecule details ›
Chain: D
Length: 12 nucleotides
Theoretical weight: 3.6 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*CP*GP*GP*AP*GP*TP*GP*TP*AP*GP*GP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 12 nucleotides
Theoretical weight: 3.74 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand UNX 17 x UNX
Ligand CA 1 x CA
1 modified residue:
Ligand 5CM 1 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.1
Spacegroup: P212121
Unit cell:
a: 40.47Å b: 51.976Å c: 66.304Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.229 0.226 0.255
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Emerging Insights into the Distinctive Neuronal Methylome.
Clemens et al. (2020)
9 other articles

2 mentions without citation

Chemical Decorations of "MARs" Residents in Orchestrating Eukaryotic Gene Regulation.
Roychowdhury et al. (2020)
1 more