7XUZ

Crystal structure of a HDAC4-MEF2A-DNA ternary complex

• PDB DOI: https://doi.org/10.2210/pdb7XUZ/pdb
• NAKB: 7XUZ

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-05-20 Released: 2023-11-29 
• Deposition Author(s): Dai, S.Y., Guo, L., Dey, R., Guo, M., Bates, D., Cayford, J., Chen, X.J., Wei, X.D., Chen, L., Chen, Y.H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.59 Å
• R-Value Free: 0.298 
• R-Value Work: 0.256 
• R-Value Observed: 0.261 

Literature

Structural insights into transcription regulation by the higher-order HDAC4-MEF2-DNA complex

Dai, S.Y., Guo, L., Dey, R., Guo, M., Bates, D., Cayford, J., Jiang, L.Y., Wei, H.D., Chen, L., Chen, Y.H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A4B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 96.09 kDa 
• Atom Count: 5,825 
• Modelled Residue Count: 627 
• Deposited Residue Count: 714 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone deacetylase 4	A [auth B], F [auth A]	133	Homo sapiens	Mutation(s): 0  Gene Names: HDAC4, KIAA0288 EC: 3.5.1.98
UniProt & NIH Common Fund Data Resources
Find proteins for P56524 (Homo sapiens) Explore P56524  Go to UniProtKB:  P56524
PHAROS:  P56524 GTEx:  ENSG00000068024

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
myocyte-specific enhancer factor 2A isoform X4	B [auth C], C [auth D], G, H	97	Homo sapiens	Mutation(s): 0  Gene Names: MEF2A
UniProt & NIH Common Fund Data Resources
Find proteins for Q02078 (Homo sapiens) Explore Q02078  Go to UniProtKB:  Q02078
PHAROS:  Q02078 GTEx:  ENSG00000068305

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*A)-3')	D [auth E], I	15	Homo sapiens

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*T)-3')	E [auth F], J	15	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.59 Å
• R-Value Free: 0.298 
• R-Value Work: 0.256 
• R-Value Observed: 0.261 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.21	α = 90
b = 93.21	β = 90
c = 224.92	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-29 
Deposition Author(s): Dai, S.Y., Guo, L., Dey, R., Guo, M., Bates, D., Cayford, J., Chen, X.J., Wei, X.D., Chen, L., Chen, Y.H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81974074,82172654
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	HL076334, GM064642

Revision History  

• Version 1.0: 2023-11-29
  Type: Initial release