› 8q9p

X-ray diffraction
2.2Å resolution

Crystal Structure of the MADS-box/MEF2 Domain of MEF2D bound to dsDNA and HDAC5 deacetylase binding motif

Released:
DOI: 10.2210/pdb8q9p/pdb
PDB entry 8q9p coloured by chain, front view.
PDB entry 8q9p coloured by chain, side view.
PDB entry 8q9p coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Folding of Class IIa HDAC Derived Peptides into α-helices Upon Binding to Myocyte Enhancer Factor-2 in Complex with DNA.
Chinellato M, Perin S, Carli A, Lastella L, Biondi B, Borsato G, Di Giorgio E, Brancolini C, Cendron L, Angelini A
J Mol Biol 436 168541 (2024)
PMID: 38492719

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-243071 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
HDAC5 (histone deacetylase 5) binding motif peptide: TRP-GLY-SER-GLY-GLU-VAL-LYS-LEU-ARG-LEU-GLN-GLU-PHE-LEU-LEU-SER-LYS-SER Chain: X
Molecule details ›
Chain: X
Length: 18 amino acids
Theoretical weight: 2.08 KDa
Source organism: Homo sapiens
Expression system: synthetic construct
MADS-box domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 95 amino acids
Theoretical weight: 11.25 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q05BX2 (Residues: 1-95; Coverage: 68%)
Gene name: MEF2D
Sequence domains: SRF-type transcription factor (DNA-binding and dimerisation domain)
MADS box dsDNA fw: AACTATTTATAAGA Chain: K
Molecule details ›
Chain: K
Length: 14 nucleotides
Theoretical weight: 4.29 KDa
MADS box dsNA rev:TCTTATAAATAGTT Chain: L
Molecule details ›
Chain: L
Length: 14 nucleotides
Theoretical weight: 4.27 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: P212121
Unit cell:
a: 54.243Å b: 56.748Å c: 76.689Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.204 0.201 0.262
Expression systems:
  • synthetic construct
  • Escherichia coli BL21(DE3)

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