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Crystal structure of WT hMBD4 complexed with T:G mismatch DNA

X-ray diffraction
2.02Å resolution
PDB entry 6vjw coloured by chain, front view.
PDB entry 6vjw coloured by chain, side view.
PDB entry 6vjw coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero trimer (preferred)
Entry contents: 1 distinct polypeptide molecule
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Methyl-CpG-binding domain protein 4 and DNA
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Multimeric state: hetero trimer
Accessible surface area: 10061.11 Å2
Buried surface area: 3539.12 Å2
Dissociation area: 1,247.98 Å2
Dissociation energy (ΔGdiss): 20.25 kcal/mol
Dissociation entropy (TΔSdiss): 10.2 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-120778

Macromolecules

Methyl-CpG-binding domain protein 4
Chain: A
Length: 138 amino acids
Theoretical weight: 16.61 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O95243 (Residues: 438-575; Coverage: 24%)
Gene names: MBD4, MED1
InterPro:
Methyl-CpG-binding domain protein 4 in PDB entry 6vjw, assembly 1, front view.
Methyl-CpG-binding domain protein 4 in PDB entry 6vjw, assembly 1, side view.
Methyl-CpG-binding domain protein 4 in PDB entry 6vjw, assembly 1, top view.
PDBe-KB: UniProt Coverage View: O95243  
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DNA chain C
Name: DNA (5'-D(*CP*CP*AP*GP*CP*GP*(ORP)P*GP*CP*AP*GP*C)-3')
Representative chains: C
Source organism: Homo sapiens [9606]
Expression system: Not provided
Length: 12 nucleotides
Theoretical weight: 3.54 KDa
DNA (5'-D(*CP*CP*AP*GP*CP*GP*(ORP)P*GP*CP*AP*GP*C)-3') in PDB entry 6vjw, assembly 1, front view.
DNA (5'-D(*CP*CP*AP*GP*CP*GP*(ORP)P*GP*CP*AP*GP*C)-3') in PDB entry 6vjw, assembly 1, side view.
DNA (5'-D(*CP*CP*AP*GP*CP*GP*(ORP)P*GP*CP*AP*GP*C)-3') in PDB entry 6vjw, assembly 1, top view.
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DNA chain D
Name: DNA (5'-D(*GP*CP*TP*GP*CP*GP*CP*GP*CP*TP*GP*G)-3')
Representative chains: D
Source organism: Homo sapiens [9606]
Expression system: Not provided
Length: 12 nucleotides
Theoretical weight: 3.7 KDa
DNA (5'-D(*GP*CP*TP*GP*CP*GP*CP*GP*CP*TP*GP*G)-3') in PDB entry 6vjw, assembly 1, front view.
DNA (5'-D(*GP*CP*TP*GP*CP*GP*CP*GP*CP*TP*GP*G)-3') in PDB entry 6vjw, assembly 1, side view.
DNA (5'-D(*GP*CP*TP*GP*CP*GP*CP*GP*CP*TP*GP*G)-3') in PDB entry 6vjw, assembly 1, top view.
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