8PDE: MADS-box/MEF2 Domain of MEF2D

Crystal Structure of the MADS-box/MEF2 Domain of MEF2D bound to dsDNA and HDAC4 deacetylase binding motif. Determined by X-ray diffraction at 2.4 Å resolution. Released 17 Apr 2024.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 10
Atoms: 4,476
Mol. weight: 66.01 kDa
Released: 17 Apr 2024

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

Secondary structure: helices and β-sheets

8PDE contains 15 α-helices and 12 β-strands across 6 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	62-69	8
β-strand	77-80	4	1
α-helix	81-89	9

Chains B and E: 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	77-80	4	1
α-helix	81-91	11

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	170-179	10

Chain D: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
α-helix	14-38	25
β-strand	42-48	7	2
β-strand	54-58	5	2
α-helix	62-71	10
β-strand	77-80	4	2
α-helix	81-91	11

Chain X: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	168-180	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MEF2D protein	A, B, D, E	protein	95	Homo sapiens	Q05BX2 (AlphaFold model)
HDAC4 (histone deacetylase 4) binding motif peptide:GSGEVKMKLQEFVLNKK	C, X	protein	17	Homo sapiens	P56524 (AlphaFold model)
DNA (5'-d(papapcptpaptptptpaptpapapgpa)-3')	F, K	DNA	14	Homo sapiens
DNA (5'-d(ptpcptptpaptpapapaptpapgptpt)-3')	G, L	DNA	14	Homo sapiens

Sequence of entity 1 (A, B, D, E), FASTA

>8PDE_1 MEF2D protein (chains A, B, D, E)
MGRKKIQIQRITDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNHSNKLFQYAST
DMDKVLLKYTEYNEPHESRTNADIIETLRKKGFNG

Sequence of entity 2 (C, X), FASTA

>8PDE_2 HDAC4 (histone deacetylase 4) binding motif peptide:GSGEVKMKLQEFVLNKK (chains C, X)
GSGEVKMKLQEFVLNKK

Sequence of entity 3 (F, K), FASTA

>8PDE_3 DNA (5'-D(P*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*GP*A)-3') (chains F, K)
AACTATTTATAAGA

Sequence of entity 4 (G, L), FASTA

>8PDE_4 DNA (5'-D(P*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*TP*T)-3') (chains G, 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 Q05BX2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8Q9N 1.51 Å, Crystal Structure of the MADS-box/MEF2 Domain of MEF2D bound to dsDNA and MITR…
8Q9Q 2.11 Å, Crystal Structure of the MADS-box/MEF2 Domain of MEF2D bound to dsDNA and HDAC7…
8Q9P 2.2 Å, Crystal Structure of the MADS-box/MEF2 Domain of MEF2D bound to dsDNA and HDAC5…
8Q9R 2.25 Å, Crystal structure of MADS-box/MEF2D N-terminal domain bound to dsDNA and HDAC9…

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