8Q9R: MADS-box/MEF2D N-terminal domain

Crystal structure of MADS-box/MEF2D N-terminal domain bound to dsDNA and HDAC9 deacetylase binding motif. Determined by X-ray diffraction at 2.25 Å resolution. Released 17 Apr 2024.

Method: X-ray diffraction
Resolution: 2.25 Å
Organisms: Homo sapiens, DNA molecule
Chains: 10
Atoms: 4,451
Mol. weight: 66.26 kDa
Released: 17 Apr 2024

Explore 8Q9R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Q9R contains 14 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	14-39	26
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 B: 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	81-90	10

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	140-153	14

Chains E and F: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	14-38	25
β-strand	42-48	7	2
β-strand	54-58	5	2
α-helix	62-70	9
β-strand	77-80	4	2
α-helix	81-91	11

Chain X: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	140-152	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone deacetylase 9 (HDAC9) binding motif peptide: EVKQKLQEFLLSKS	C, X	protein	18	Homo sapiens	Q9UKV0 (AlphaFold model)
MEF2D protein	A, B, E, F	protein	95	Homo sapiens	Q05BX2 (AlphaFold model)
MADS box dsDNA: AACTATTTATAAGA	G, K	DNA	14	DNA molecule
MADS box dsDNA: TCTTATAAATAGT	H, L	DNA	14	DNA molecule

Sequence of entity 1 (C, X), FASTA

>8Q9R_1 Histone deacetylase 9 (HDAC9) binding motif peptide: EVKQKLQEFLLSKS (chains C, X)
WGSGEVKQKLQEFLLSKS

Sequence of entity 2 (A, B, E, F), FASTA

>8Q9R_2 MEF2D protein (chains A, B, E, F)
MGRKKIQIQRITDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNHSNKLFQYAST
DMDKVLLKYTEYNEPHESRTNADIIETLRKKGFNG

Sequence of entity 3 (G, K), FASTA

>8Q9R_3 MADS box dsDNA: AACTATTTATAAGA (chains G, K)
AACTATTTATAAGA

Sequence of entity 4 (H, L), FASTA

>8Q9R_4 MADS box dsDNA: TCTTATAAATAGT (chains H, 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 Q9UKV0 (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…

Browse structure collections

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