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- PDB-8pde: Crystal Structure of the MADS-box/MEF2 Domain of MEF2D bound to d... -

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Basic information

Entry
Database: PDB / ID: 8pde
TitleCrystal Structure of the MADS-box/MEF2 Domain of MEF2D bound to dsDNA and HDAC4 deacetylase binding motif
Components
  • DNA (5'-D(P*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*GP*A)-3')
  • DNA (5'-D(P*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*TP*T)-3')
  • HDAC4 (histone deacetylase 4) binding motif peptide:GSGEVKMKLQEFVLNKK
  • MEF2D protein
KeywordsDNA BINDING PROTEIN / Myocyte enhancer factor 2 / Class II Histone deacetylase
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChinellato, M. / Carli, A. / Perin, S. / Mazzocato, Y. / Biondi, B. / Di Giorgio, E. / Brancolini, C. / Angelini, A. / Cendron, L.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of Education2017JL8SRX_005 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
DepositionJun 12, 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
A: MEF2D protein
B: MEF2D protein
C: HDAC4 (histone deacetylase 4) binding motif peptide:GSGEVKMKLQEFVLNKK
D: MEF2D protein
E: MEF2D protein
F: DNA (5'-D(P*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*GP*A)-3')
G: DNA (5'-D(P*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*TP*T)-3')
X: HDAC4 (histone deacetylase 4) binding motif peptide:GSGEVKMKLQEFVLNKK
K: DNA (5'-D(P*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*GP*A)-3')
L: DNA (5'-D(P*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)66,00610
Polymers66,00610
Non-polymers00
Water1,08160
1
A: MEF2D protein
B: MEF2D protein
X: HDAC4 (histone deacetylase 4) binding motif peptide:GSGEVKMKLQEFVLNKK
K: DNA (5'-D(P*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*GP*A)-3')
L: DNA (5'-D(P*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)33,0035
Polymers33,0035
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11770 Å2
ΔGint-78 kcal/mol
Surface area13970 Å2
2
C: HDAC4 (histone deacetylase 4) binding motif peptide:GSGEVKMKLQEFVLNKK
D: MEF2D protein
E: MEF2D protein
F: DNA (5'-D(P*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*GP*A)-3')
G: DNA (5'-D(P*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)33,0035
Polymers33,0035
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11440 Å2
ΔGint-77 kcal/mol
Surface area13980 Å2
Unit cell
Length a, b, c (Å)57.024, 76.330, 56.240
Angle α, β, γ (deg.)90.00, 92.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: 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 traceable in the electron density maps
Source: (gene. exp.) Homo sapiens (human) / Gene: MEF2D / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q05BX2
#2: Protein/peptide HDAC4 (histone deacetylase 4) binding motif peptide:GSGEVKMKLQEFVLNKK


Mass: 1939.322 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: synthetic peptide: missing residues are not traceable in the electron density maps
Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*GP*A)-3')


Mass: 4286.842 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain DNA (5'-D(P*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*TP*T)-3')


Mass: 4268.813 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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

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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 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: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.4→45.65 Å / Num. obs: 17911 / % possible obs: 94.7 % / Redundancy: 4.1 % / CC1/2: 0.992 / Rmerge(I) obs: 0.132 / Net I/σ(I): 7
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.865 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1938 / CC1/2: 0.533

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→45.65 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.279 --
Rwork0.217 --
obs-17911 94.7 %
Refinement stepCycle: LAST / Resolution: 2.4→45.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3268 1148 0 60 4476

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