› 3c2i

X-ray diffraction
2.5Å resolution

The Crystal Structure of Methyl-CpG Binding Domain of Human MeCP2 in Complex with a Methylated DNA Sequence from BDNF

Released:
DOI: 10.2210/pdb3c2i/pdb
PDB entry 3c2i coloured by chain, front view.
PDB entry 3c2i coloured by chain, side view.
PDB entry 3c2i coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
MeCP2 binding to DNA depends upon hydration at methyl-CpG.
Ho KL, McNae IW, Schmiedeberg L, Klose RJ, Bird AP, Walkinshaw MD
Mol Cell 29 525-31 (2008)
PMID: 18313390

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-116120 (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: 97 amino acids
Theoretical weight: 11.28 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(*DTP*DCP*DTP*DGP*DGP*DAP*DAP*(5CM)P*DGP*DGP*DAP*DAP*DTP*DTP*DCP*DTP*DTP*DCP*DTP*DA)-3') Chain: B
Molecule details ›
Chain: B
Length: 20 nucleotides
Theoretical weight: 6.14 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*DAP*DTP*DAP*DGP*DAP*DAP*DGP*DAP*DAP*DTP*DTP*DCP*(5CM)P*DGP*DTP*DTP*DCP*DCP*DAP*DG)-3') Chain: C
Molecule details ›
Chain: C
Length: 20 nucleotides
Theoretical weight: 6.16 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

No bound ligands
2 modified residues:
Ligand MSE 2 x MSE
Ligand 5CM 2 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM14
Spacegroup: C2
Unit cell:
a: 79.71Å b: 53.6Å c: 65.73Å
α: 90° β: 132.1° γ: 90°
R-values:
R R work R free
0.215 0.212 0.276
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

46 review citations

The role of MeCP2 in the brain.
Guy et al. (2011)
45 more

38 mentions without citation

On how mammalian transcription factors recognize methylated DNA.
Buck-Koehntop et al. (2013)
37 more