6BYY: MEF2 CHIMERA/DNA Complex

MEF2 CHIMERA/DNA Complex. Determined by X-ray diffraction at 2.3 Å resolution. Released 31 Jan 2018.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 8
Atoms: 4,375
Mol. weight: 63.85 kDa
Ligands: 1PG, TCE
Released: 31 Jan 2018

Explore 6BYY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6BYY contains 13 α-helices and 12 β-strands across 4 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	77-79	3	1
α-helix	81-89	9

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	62-70	9
β-strand	77-80	4	1
α-helix	81-91	11

Chain C: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
α-helix	14-39	26
β-strand	42-48	7	2
β-strand	54-58	5	2
α-helix	62-71	10
β-strand	77-79	3	2
α-helix	81-89	9

Chain D: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	14-39	26
β-strand	42-48	7	2
β-strand	54-58	5	2
α-helix	62-70	9
β-strand	77-79	3	2
α-helix	81-87	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MEF2 chimera	A, B, C, D	protein	95	Homo sapiens	Q02078 (AlphaFold model), Q02080 (AlphaFold model)
DNA (5'-d(papapcptpaptptptpaptpapapgpa)-3')	E, K	DNA	14	Homo sapiens
DNA (5'-d(ptptpcptptpaptpapapaptpapgptp*t)-3')	F, L	DNA	15	Homo sapiens

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

>6BYY_1 MEF2 CHIMERA (chains A, B, C, D)
MGRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYAST
DMDKVLLKYTEYSEPHESRTNTDILETLKRREHRG

Sequence of entity 2 (E, K), FASTA

>6BYY_2 DNA (5'-D(P*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*GP*A)-3') (chains E, K)
AACTATTTATAAGA

Sequence of entity 3 (F, L), FASTA

>6BYY_3 DNA (5'-D(P*TP*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*TP*T)-3') (chains F, L)
TTCTTATAAATAGTT

Ligands and cofactors

ID	Name	Formula	Copies
1PG	2-(2-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethanol	C11 H24 O6	2
TCE	3,3',3''-phosphanetriyltripropanoic acid	C9 H15 O6 P	1

Primary citation

The Cancer Mutation D83V Induces an alpha-Helix to beta-Strand Conformation Switch in MEF2B. Lei, X., Kou, Y., Fu, Y. et al. J Mol Biol (2018) 430:1157-1172. DOI 10.1016/j.jmb.2018.02.012 · PubMed

Other PDB entries of the same protein (UniProt Q02078 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1EGW 1.5 Å, Crystal structure of MEF2A core bound to DNA
6WC2 2.1 Å, Crystal Structure of a Ternary MEF2 Chimera/NKX2-5/myocardin enhancer DNA Complex
3P57 2.19 Å, Crystal structure of the p300 TAZ2 domain bound to MEF2 on DNA
1LEW 2.3 Å, Crystal structure of map kinase P38 complexed to the docking site on its nuclear…
3MU6 2.43 Å, Inhibiting the Binding of Class IIa Histone Deacetylases to Myocyte Enhancer Factor-2 by…
3KOV 2.9 Å, Structure of MEF2A bound to DNA reveals a completely folded MADS-box/MEF2 domain that…
6BZ1 2.97 Å, MEF2 Chimera D83V mutant/DNA complex
7XUZ 3.59 Å, Crystal structure of a HDAC4-MEF2A-DNA ternary complex
1C7U Complex of the DNA binding core domain of the transcription factor MEF2A with a 20mer…

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