7XUZ: HDAC4-MEF2A-DNA ternary complex

Name: PDB 7XUZ: Crystal structure of a HDAC4-MEF2A-DNA ternary complex
Published: 2023-11-29
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

Crystal structure of a HDAC4-MEF2A-DNA ternary complex. Determined by X-ray diffraction at 3.59 Å resolution. Released 29 Nov 2023.

Method: X-ray diffraction
Resolution: 3.59 Å
Organism: Homo sapiens
Chains: 10
Atoms: 5,825
Mol. weight: 96.09 kDa
Released: 29 Nov 2023

Explore 7XUZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7XUZ contains 19 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: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	68-145	78
α-helix	147-150	4
α-helix	153-156	4
α-helix	171-179	9

Chain B: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	68-156	89
α-helix	171-179	9

Chains C and G: 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	63-69	7
β-strand	77-79	3	1
α-helix	81-85	5

Chain D: 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	77-79	3	1
α-helix	81-88	8

Chain H: 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	62-69	8
β-strand	77-80	4	2
α-helix	81-88	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone deacetylase 4	A, B	protein	133	Homo sapiens	P56524 (AlphaFold model)
myocyte-specific enhancer factor 2A isoform X4	C, D, G, H	protein	97	Homo sapiens	Q02078 (AlphaFold model)
DNA (5'-d(papcptpaptptptpaptpap*a)-3')	E, I	DNA	15	Homo sapiens
DNA (5'-d(tpcptptpaptpapapaptpapgp*t)-3')	F, J	DNA	15	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>7XUZ_1 Histone deacetylase 4 (chains A, B)
GPAEPALREQQLQQELLALKQKQQIQRQILIAEFQRQHEQLSRQHEAQLHEHIKQQQEML
AMKHQQELLEHQRKLERHRQEQELEKQHREQKLQQLKNKEKGKESAVASTEVKMKLQEFV
LNKKKALAHRNLN

Sequence of entity 2 (C, D, G, H), FASTA

>7XUZ_2 myocyte-specific enhancer factor 2A isoform X4 (chains C, D, G, H)
GPMGRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYA
STDMDKVLLKYTEYNEPHESRTNSDIVEALNKKEHRG

Sequence of entity 3 (E, I), FASTA

>7XUZ_3 DNA (5'-D(P*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*A)-3') (chains E, I)
AAACTATTTATAAGA

Sequence of entity 4 (F, J), FASTA

>7XUZ_4 DNA (5'-D(*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*T)-3') (chains F, J)
TCTTATAAATAGTTT

Primary citation

Structural insights into the HDAC4-MEF2A-DNA complex and its implication in long-range transcriptional regulation. Dai, S., Guo, L., Dey, R. et al. Nucleic Acids Res (2024) 52:2711-2723. DOI 10.1093/nar/gkae036 · PubMed

Other PDB entries of the same protein (UniProt P56524 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3V31 1.57 Å, Crystal Structure of the Peptide Bound Complex of the Ankyrin Repeat Domains of Human…
2VQM 1.8 Å, Structure of HDAC4 catalytic domain bound to a hydroxamic acid inhbitor
3UXG 1.85 Å, Crystal structure of RFXANK
5ZOO 1.85 Å, Crystal structure of histone deacetylase 4 (HDAC4) in complex with a SMRT corepressor…
3UZD 1.86 Å, Crystal structure of 14-3-3 GAMMA
2VQQ 1.9 Å, Structure of HDAC4 catalytic domain (a double cysteine-to-alanine mutant) bound to a…
2VQJ 2.1 Å, Structure of HDAC4 catalytic domain bound to a trifluoromethylketone inhbitor
2VQO 2.15 Å, Structure of HDAC4 catalytic domain with a gain-of-function muation bound to a…
6FYZ 2.15 Å, Development and characterization of a CNS-penetrant benzhydryl hydroxamic acid class IIa…
8PDE 2.4 Å, Crystal Structure of the MADS-box/MEF2 Domain of MEF2D bound to dsDNA and HDAC4…
2H8N 2.6 Å, Structure of a glutamine-rich domain from histone deacetylase 4
5A2S 2.65 Å, Potent, selective and CNS-penetrant tetrasubstituted cyclopropane class IIa histone…

Browse structure collections

About this viewer

MolViewer shows 7XUZ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.