8Q9P: MADS-box/MEF2 Domain of MEF2D

Crystal Structure of the MADS-box/MEF2 Domain of MEF2D bound to dsDNA and HDAC5 deacetylase binding motif. Determined by X-ray diffraction at 2.2 Å resolution. Released 17 Apr 2024.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 5
Atoms: 2,260
Mol. weight: 33.14 kDa
Released: 17 Apr 2024

Explore 8Q9P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Q9P contains 7 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: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	14-38	25
β-strand	42-48	7	1
β-strand	54-58	5	1
α-helix	62-71	10
β-strand	77-79	3	1
α-helix	81-91	11

Chain B: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	14-39	26
β-strand	42-48	7	1
β-strand	54-58	5	1
α-helix	62-71	10
β-strand	77-79	3	1
α-helix	81-90	10

Chain X: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	183-192	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HDAC5 (histone deacetylase 5) binding motif peptide: TRP-GLY-SER-GLY-GLU-VAL-LYS-LEU-ARG-LEU-GLN-GL…	X	protein	18	Homo sapiens	Q9UQL6 (AlphaFold model)
MEF2D protein	A, B	protein	95	Homo sapiens	Q05BX2 (AlphaFold model)
MADS box dsDNA fw: AACTATTTATAAGA	K	DNA	14	Homo sapiens
MADS box dsNA rev:TCTTATAAATAGTT	L	DNA	14	Homo sapiens

Sequence of entity 1 (X), FASTA

>8Q9P_1 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 (chains X)
WGSGEVKLRLQEFLLSKS

Sequence of entity 2 (A, B), FASTA

>8Q9P_2 MEF2D protein (chains A, B)
MGRKKIQIQRITDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNHSNKLFQYAST
DMDKVLLKYTEYNEPHESRTNADIIETLRKKGFNG

Sequence of entity 3 (K), FASTA

>8Q9P_3 MADS box dsDNA fw: AACTATTTATAAGA (chains K)
AACTATTTATAAGA

Sequence of entity 4 (L), FASTA

>8Q9P_4 MADS box dsNA rev: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 Q9UQL6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5UWI 2.14 Å, Crystal Structure of HDAC5 NES Peptide in complex with CRM1-Ran-RanBP1

Browse structure collections

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