6WC5: Myocyte-specific enhancer factor 2B

Crystal Structure of a Ternary MEF2B/NKX2-5/myocardin enhancer DNA Complex. Determined by X-ray diffraction at 2.9 Å resolution. Released 22 Jul 2020.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Homo sapiens, synthetic construct
Chains: 10
Atoms: 5,705
Mol. weight: 84.04 kDa
Released: 22 Jul 2020

Explore 6WC5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6WC5 contains 20 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	62-70	9
β-strand	77-79	3	1
α-helix	81-88	8

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	77-79	3	1
α-helix	81-89	9

Chain C: 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	77-79	3	2
α-helix	81-89	9

Chain D: 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	62-71	10
β-strand	77-79	3	2
α-helix	81-89	9

Chain I: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	144-146	3
α-helix	147-159	13
α-helix	165-175	11
α-helix	179-194	16

Chain N: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	148-159	12
α-helix	165-175	11
α-helix	179-193	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Myocyte-specific enhancer factor 2B	A, B, C, D	protein	90	Homo sapiens	Q02080 (AlphaFold model)
Myocardin enhancer DNA	E, G	DNA	22	synthetic construct
Myocardin enhancer DNA	F, H	DNA	22	synthetic construct
Homeobox protein Nkx-2.5	I, N	protein	57	Homo sapiens	P52952 (AlphaFold model)

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

>6WC5_1 Myocyte-specific enhancer factor 2B (chains A, B, C, D)
GRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYASTD
MDRVLLKYTEYSEPHESRTNTDILETLKRR

Sequence of entity 2 (E, G), FASTA

>6WC5_2 Myocardin enhancer DNA (chains E, G)
AAGCACTTTCTTAAAATAGTGG

Sequence of entity 3 (F, H), FASTA

>6WC5_3 Myocardin enhancer DNA (chains F, H)
CCACTATTTTAAGAAAGTGCTT

Sequence of entity 4 (I, N), FASTA

>6WC5_4 Homeobox protein Nkx-2.5 (chains I, N)
KPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSKRQ

Primary citation

Crystal Structures of Ternary Complexes of MEF2 and NKX2-5 Bound to DNA Reveal a Disease Related Protein-Protein Interaction Interface. Lei, X., Zhao, J., Sagendorf, J.M. et al. J Mol Biol (2020) 432:5499-5508. DOI 10.1016/j.jmb.2020.07.004 · PubMed

Other PDB entries of the same protein (UniProt Q02080 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6WC2 2.1 Å, Crystal Structure of a Ternary MEF2 Chimera/NKX2-5/myocardin enhancer DNA Complex
1N6J 2.2 Å, Structural basis of sequence-specific recruitment of histone deacetylases by Myocyte…
6BYY 2.3 Å, MEF2 CHIMERA/DNA Complex
6C9L 2.3 Å, MEF2B Apo Protein Structure
1TQE 2.7 Å, Mechanism of recruitment of class II histone deacetylases by myocyte enhancer factor-2
6BZ1 2.97 Å, MEF2 Chimera D83V mutant/DNA complex

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