8Q9Q: MADS-box/MEF2 Domain of MEF2D

Crystal Structure of the MADS-box/MEF2 Domain of MEF2D bound to dsDNA and HDAC7 deacetylase binding motif. Determined by X-ray diffraction at 2.11 Å resolution. Released 17 Apr 2024.

Method: X-ray diffraction
Resolution: 2.11 Å
Organisms: Homo sapiens, DNA molecule
Chains: 5
Atoms: 2,262
Mol. weight: 32.75 kDa
Released: 17 Apr 2024

Explore 8Q9Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Q9Q contains 9 α-helices and 6 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
α-helix	14-38	25
β-strand	42-48	7	1
β-strand	54-58	5	1
α-helix	62-70	9
β-strand	77-79	3	1
α-helix	81-90	10

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
α-helix	14-38	25
β-strand	42-48	7	1
β-strand	54-58	5	1
α-helix	62-70	9
β-strand	77-80	4	1
α-helix	81-89	9

Chain X: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	84-93	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HDAC7 (histone deacetylase 7) binding motif peptide: GLY-VAL-VAL-LYS-GLN-LYS-LEU-ALA-GLU-VAL-ILE-LE…	X	protein	15	Homo sapiens	Q8WUI4 (AlphaFold model)
MEF2D protein	A, B	protein	95	Homo sapiens	Q05BX2 (AlphaFold model)
MADS box dsDNA: AACTATTTATAAGA	K	DNA	14	DNA molecule
MADS box dsDNA: TCTTATAAATAGTT	L	DNA	14	DNA molecule

Sequence of entity 1 (X), FASTA

>8Q9Q_1 HDAC7 (histone deacetylase 7) binding motif peptide: GLY-VAL-VAL-LYS-GLN-LYS-LEU-ALA-GLU-VAL-ILE-LEU-LYS-LYS-GLN (chains X)
GVVKQKLAEVILKKQ

Sequence of entity 2 (A, B), FASTA

>8Q9Q_2 MEF2D protein (chains A, B)
MGRKKIQIQRITDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNHSNKLFQYAST
DMDKVLLKYTEYNEPHESRTNADIIETLRKKGFNG

Sequence of entity 3 (K), FASTA

>8Q9Q_3 MADS box dsDNA: AACTATTTATAAGA (chains K)
AACTATTTATAAGA

Sequence of entity 4 (L), FASTA

>8Q9Q_4 MADS box dsDNA: TCTTATAAATAGTT (chains L)
TCTTATAAATAGTT

Primary citation

Folding of Class IIa HDAC Derived Peptides into alpha-helices Upon Binding to Myocyte Enhancer Factor-2 in Complex with DNA. Chinellato, M., Perin, S., Carli, A. et al. J Mol Biol (2024) 436:168541-168541. DOI 10.1016/j.jmb.2024.168541 · PubMed

Other PDB entries of the same protein (UniProt Q8WUI4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3C10 2.0 Å, Crystal structure of catalytic domain of human histone deacetylase HDAC7 in complex with…
3C0Y 2.1 Å, Crystal structure of catalytic domain of human histone deacetylase HDAC7
3C0Z 2.1 Å, Crystal structure of catalytic domain of human histone deacetylase HDAC7 in complex with…
3ZNR 2.4 Å, HDAC7 bound with inhibitor TMP269
3ZNS 2.45 Å, HDAC7 bound with TFMO inhibitor tmp942

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