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- PDB-7xuz: Crystal structure of a HDAC4-MEF2A-DNA ternary complex -

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Basic information

Entry
Database: PDB / ID: 7xuz
TitleCrystal structure of a HDAC4-MEF2A-DNA ternary complex
Components
  • DNA (5'-D(*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*T)-3')
  • DNA (5'-D(P*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*A)-3')
  • Histone deacetylase 4
  • myocyte-specific enhancer factor 2A isoform X4
KeywordsTRANSCRIPTION / HDAC4 / MEF2 / transcription repressor
Function / homology
Function and homology information


RUNX2 regulates chondrocyte maturation / response to denervation involved in regulation of muscle adaptation / negative regulation of myotube differentiation / peptidyl-lysine deacetylation / positive regulation of protein sumoylation / regulation of protein binding / negative regulation of transcription by competitive promoter binding / protein deacetylation / cardiac muscle hypertrophy in response to stress / histone deacetylase ...RUNX2 regulates chondrocyte maturation / response to denervation involved in regulation of muscle adaptation / negative regulation of myotube differentiation / peptidyl-lysine deacetylation / positive regulation of protein sumoylation / regulation of protein binding / negative regulation of transcription by competitive promoter binding / protein deacetylation / cardiac muscle hypertrophy in response to stress / histone deacetylase / protein lysine deacetylase activity / negative regulation of glycolytic process / SUMO transferase activity / negative regulation of gene expression, epigenetic / histone deacetylase activity / type I interferon-mediated signaling pathway / B cell activation / Notch-HLH transcription pathway / potassium ion binding / RUNX3 regulates p14-ARF / histone deacetylase complex / protein sumoylation / transcription repressor complex / SUMOylation of chromatin organization proteins / response to interleukin-1 / B cell differentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / negative regulation of DNA-binding transcription factor activity / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / positive regulation of DNA-binding transcription factor activity / histone deacetylase binding / nervous system development / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / molecular adaptor activity / protein dimerization activity / nuclear speck / chromatin remodeling / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-templated transcription / positive regulation of cell population proliferation / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Holliday junction regulator protein family C-terminal / Holliday junction regulator protein family C-terminal repeat / Histone deacetylase, glutamine rich N-terminal domain / Glutamine rich N terminal domain of histone deacetylase 4 / : / MADS MEF2-like / Transcription factor, MADS-box / Transcription factor, MADS-box superfamily / SRF-type transcription factor (DNA-binding and dimerisation domain) / MADS-box domain signature. ...Holliday junction regulator protein family C-terminal / Holliday junction regulator protein family C-terminal repeat / Histone deacetylase, glutamine rich N-terminal domain / Glutamine rich N terminal domain of histone deacetylase 4 / : / MADS MEF2-like / Transcription factor, MADS-box / Transcription factor, MADS-box superfamily / SRF-type transcription factor (DNA-binding and dimerisation domain) / MADS-box domain signature. / MADS-box domain profile. / MADS / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Myocyte-specific enhancer factor 2A isoform X4 / Histone deacetylase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.591 Å
AuthorsDai, S.Y. / Guo, L. / Dey, R. / Guo, M. / Bates, D. / Cayford, J. / Chen, X.J. / Wei, X.D. / Chen, L. / Chen, Y.H.
Funding support China, United States, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81974074,82172654 China
National Institutes of Health/National Cancer Institute (NIH/NCI)HL076334, GM064642 United States
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Structural insights into the HDAC4-MEF2A-DNA complex and its implication in long-range transcriptional regulation.
Authors: Dai, S. / Guo, L. / Dey, R. / Guo, M. / Zhang, X. / Bates, D. / Cayford, J. / Jiang, L. / Wei, H. / Chen, Z. / Zhang, Y. / Chen, L. / Chen, Y.
History
DepositionMay 20, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Histone deacetylase 4
C: myocyte-specific enhancer factor 2A isoform X4
D: myocyte-specific enhancer factor 2A isoform X4
E: DNA (5'-D(P*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*A)-3')
F: DNA (5'-D(*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*T)-3')
A: Histone deacetylase 4
G: myocyte-specific enhancer factor 2A isoform X4
H: myocyte-specific enhancer factor 2A isoform X4
I: DNA (5'-D(P*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*A)-3')
J: DNA (5'-D(*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)96,09010
Polymers96,09010
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24820 Å2
ΔGint-177 kcal/mol
Surface area44580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.210, 93.210, 224.920
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Histone deacetylase 4 / HD4


Mass: 16081.415 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC4, KIAA0288 / Production host: Escherichia coli (E. coli) / References: UniProt: P56524, histone deacetylase
#2: Protein
myocyte-specific enhancer factor 2A isoform X4


Mass: 11395.182 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MEF2A / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6J2KXN9
#3: DNA chain DNA (5'-D(P*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*A)-3')


Mass: 4600.049 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain DNA (5'-D(*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*T)-3')


Mass: 4573.006 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0 mM HEPES pH 7.5, 0.2 M NaCl, 3% (v/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.59→40.363 Å / Num. obs: 12749 / % possible obs: 98.03 % / Redundancy: 7.9 % / Biso Wilson estimate: 124.14 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 19.51
Reflection shellResolution: 3.59→3.73 Å / Rmerge(I) obs: 0.521 / Num. unique obs: 1183

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TQE,2H8N

1tqe

2h8n


Resolution: 3.591→40.361 Å / SU ML: 0.76 / Cross valid method: THROUGHOUT / σ(F): 2.25 / Phase error: 43.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.298 1260 9.94 %
Rwork0.2561 11415 -
obs0.2605 12675 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 413.57 Å2 / Biso mean: 191.1628 Å2 / Biso min: 57.97 Å2
Refinement stepCycle: final / Resolution: 3.591→40.361 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4833 996 0 0 5829
Num. residues----627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026002
X-RAY DIFFRACTIONf_angle_d0.458226
X-RAY DIFFRACTIONf_chiral_restr0.032910
X-RAY DIFFRACTIONf_plane_restr0.001891
X-RAY DIFFRACTIONf_dihedral_angle_d15.4693589
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.591-3.73450.61771360.5271118592
3.7345-3.90430.41891370.3872127499
3.9043-4.10990.32591370.2854126699
4.1099-4.36720.33661410.25571276100
4.3672-4.70390.3061400.23881293100
4.7039-5.17640.29911460.2144128199
5.1764-5.92340.29741390.25661274100
5.9234-7.45520.33021380.29541301100
7.4552-40.3610.22241460.1994126597
Refinement TLS params.Method: refined / Origin x: -11.9547 Å / Origin y: -5.9148 Å / Origin z: 0.176 Å
111213212223313233
T0.8541 Å20.1516 Å20.0558 Å2-0.8885 Å2-0.1521 Å2--0.6877 Å2
L0.1832 °2-0.0194 °2-0.2516 °2-0.1628 °20.2994 °2---0.023 °2
S-0.067 Å °-0.1363 Å °0.0076 Å °-0.0565 Å °0.102 Å °-0.0798 Å °-0.0642 Å °0.306 Å °-0.0447 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB64 - 183
2X-RAY DIFFRACTION1allC4 - 86
3X-RAY DIFFRACTION1allD7 - 91
4X-RAY DIFFRACTION1allE3 - 13
5X-RAY DIFFRACTION1allF2 - 14
6X-RAY DIFFRACTION1allA64 - 183
7X-RAY DIFFRACTION1allG4 - 87
8X-RAY DIFFRACTION1allH2 - 91
9X-RAY DIFFRACTION1allI3 - 14
10X-RAY DIFFRACTION1allJ2 - 14

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