› 5bt2

X-ray diffraction
2.2Å resolution

MeCP2 MBD domain (A140V) in complex with methylated DNA

Released:
DOI: 10.2210/pdb5bt2/pdb
PDB entry 5bt2 coloured by chain, front view.
PDB entry 5bt2 coloured by chain, side view.
PDB entry 5bt2 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A/T Run Geometry of B-form DNA Is Independent of Bound Methyl-CpG Binding Domain, Cytosine Methylation and Flanking Sequence.
Chia JY, Tan WS, Ng CL, Hu NJ, Foo HL, Ho KL
Sci Rep 6 31210 (2016)
PMID: 27502833

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-118439 (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: 11.16 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(*TP*CP*TP*GP*GP*AP*AP*(5CM)P*GP*GP*AP*AP*TP*TP*CP*TP*TP*CP*TP*A)-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(*AP*TP*AP*GP*AP*AP*GP*AP*AP*TP*TP*CP*(5CM)P*GP*TP*TP*CP*CP*AP*G)-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
1 modified residue:
Ligand 5CM 2 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: C2
Unit cell:
a: 78.66Å b: 53.49Å c: 65.78Å
α: 90° β: 132.47° γ: 90°
R-values:
R R work R free
0.177 0.175 0.227
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 citations in other articles

Structural Basis of MeCP2 Distribution on Non-CpG Methylated and Hydroxymethylated DNA.
Sperlazza et al. (2017)

6 mentions without citation

MeCP2: The Genetic Driver of Rett Syndrome Epigenetics.
Good et al. (2021)
5 more