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- PDB-8q9r: Crystal structure of MADS-box/MEF2D N-terminal domain bound to ds... -

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Basic information

Entry
Database: PDB / ID: 8q9r
TitleCrystal structure of MADS-box/MEF2D N-terminal domain bound to dsDNA and HDAC9 deacetylase binding motif
Components
  • Histone deacetylase 9 (HDAC9) binding motif peptide: EVKQKLQEFLLSKS
  • MADS box dsDNA: AACTATTTATAAGA
  • MADS box dsDNA: TCTTATAAATAGT
  • MEF2D protein
KeywordsTRANSCRIPTION / transcriptional regulator
Function / homology
Function and homology information


animal organ development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / nervous system development / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Holliday junction regulator protein family C-terminal / Holliday junction regulator protein family C-terminal repeat / 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
Similarity search - Domain/homology
DNA / DNA (> 10) / MEF2D protein
Similarity search - Component
Biological speciesHomo sapiens (human)
DNA molecule (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsChinellato, M. / Carli, A. / Perin, S. / Mazzoccato, Y. / Di Giorgio, E. / Brancolini, C. / Angelini, A. / Cendron, L.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of EducationC94I19001550001 Italy
CitationJournal: J.Mol.Biol. / Year: 2024
Title: Folding of Class IIa HDAC Derived Peptides into alpha-helices Upon Binding to Myocyte Enhancer Factor-2 in Complex with DNA.
Authors: Chinellato, M. / Perin, S. / Carli, A. / Lastella, L. / Biondi, B. / Borsato, G. / Di Giorgio, E. / Brancolini, C. / Cendron, L. / Angelini, A.
History
DepositionAug 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Histone deacetylase 9 (HDAC9) binding motif peptide: EVKQKLQEFLLSKS
A: MEF2D protein
B: MEF2D protein
K: MADS box dsDNA: AACTATTTATAAGA
L: MADS box dsDNA: TCTTATAAATAGT
C: Histone deacetylase 9 (HDAC9) binding motif peptide: EVKQKLQEFLLSKS
E: MEF2D protein
F: MEF2D protein
G: MADS box dsDNA: AACTATTTATAAGA
H: MADS box dsDNA: TCTTATAAATAGT


Theoretical massNumber of molelcules
Total (without water)66,26210
Polymers66,26210
Non-polymers00
Water34219
1
X: Histone deacetylase 9 (HDAC9) binding motif peptide: EVKQKLQEFLLSKS
A: MEF2D protein
B: MEF2D protein
K: MADS box dsDNA: AACTATTTATAAGA
L: MADS box dsDNA: TCTTATAAATAGT


Theoretical massNumber of molelcules
Total (without water)33,1315
Polymers33,1315
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11740 Å2
ΔGint-71 kcal/mol
Surface area13830 Å2
MethodPISA
2
C: Histone deacetylase 9 (HDAC9) binding motif peptide: EVKQKLQEFLLSKS
E: MEF2D protein
F: MEF2D protein
G: MADS box dsDNA: AACTATTTATAAGA
H: MADS box dsDNA: TCTTATAAATAGT


Theoretical massNumber of molelcules
Total (without water)33,1315
Polymers33,1315
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11920 Å2
ΔGint-76 kcal/mol
Surface area13930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.391, 60.042, 77.108
Angle α, β, γ (deg.)90.00, 91.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Histone deacetylase 9 (HDAC9) binding motif peptide: EVKQKLQEFLLSKS


Mass: 2067.365 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: synthetic construct (others)
#2: Protein
MEF2D protein / Myocyte enhancer factor 2D


Mass: 11254.035 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Missing residues are not visible in the electron density maps
Source: (gene. exp.) Homo sapiens (human) / Gene: MEF2D / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q05BX2
#3: DNA chain MADS box dsDNA: AACTATTTATAAGA


Mass: 4286.842 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DNA molecule (others) / Production host: synthetic construct (others)
#4: DNA chain MADS box dsDNA: TCTTATAAATAGT


Mass: 4268.813 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DNA molecule (others) / Production host: synthetic construct (others)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 38.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 200 mM sodium formate, 100 mM Bis-Tris propane pH 6.5 and 20% w/v polyethylene glycol 3350 (PEG 3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.25→47.36 Å / Num. obs: 25008 / % possible obs: 99.7 % / Redundancy: 3.6 % / CC1/2: 0.998 / Net I/σ(I): 9
Reflection shellResolution: 2.25→2.32 Å / Rmerge(I) obs: 1.103 / Mean I/σ(I) obs: 1 / Num. unique obs: 2276 / CC1/2: 0.372

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→47.36 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 31.03 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2727 1262 5.05 %
Rwork0.2227 --
obs0.2251 24972 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→47.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3284 1148 0 19 4451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134616
X-RAY DIFFRACTIONf_angle_d1.7466416
X-RAY DIFFRACTIONf_dihedral_angle_d29.169983
X-RAY DIFFRACTIONf_chiral_restr0.187718
X-RAY DIFFRACTIONf_plane_restr0.012614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.340.36991760.32162567X-RAY DIFFRACTION100
2.34-2.450.38341240.29182657X-RAY DIFFRACTION100
2.45-2.580.31241370.2722624X-RAY DIFFRACTION100
2.58-2.740.32461440.27372626X-RAY DIFFRACTION100
2.74-2.950.371170.29442645X-RAY DIFFRACTION100
2.95-3.240.29941300.26242636X-RAY DIFFRACTION99
3.24-3.710.27521500.22922610X-RAY DIFFRACTION99
3.71-4.680.24861800.18652608X-RAY DIFFRACTION99

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