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- PDB-8q9p: Crystal Structure of the MADS-box/MEF2 Domain of MEF2D bound to d... -

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Basic information

Entry
Database: PDB / ID: 8q9p
TitleCrystal Structure of the MADS-box/MEF2 Domain of MEF2D bound to dsDNA and HDAC5 deacetylase binding motif
Components
  • HDAC5 (histone deacetylase 5) binding motif peptide: TRP-GLY-SER-GLY-GLU-VAL-LYS-LEU-ARG-LEU-GLN-GLU-PHE-LEU-LEU-SER-LYS-SER
  • MADS box dsDNA fw: AACTATTTATAAGA
  • MADS box dsNA rev:TCTTATAAATAGTT
  • MEF2D protein
KeywordsTRANSCRIPTION / transcriptional repressor
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: 2.2 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 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

Downloads & links

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Assembly

Deposited unit
X: HDAC5 (histone deacetylase 5) binding motif peptide: TRP-GLY-SER-GLY-GLU-VAL-LYS-LEU-ARG-LEU-GLN-GLU-PHE-LEU-LEU-SER-LYS-SER
A: MEF2D protein
B: MEF2D protein
K: MADS box dsDNA fw: AACTATTTATAAGA
L: MADS box dsNA rev:TCTTATAAATAGTT


Theoretical massNumber of molelcules
Total (without water)33,1445
Polymers33,1445
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, EMSA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12020 Å2
ΔGint-79 kcal/mol
Surface area14340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.243, 56.748, 76.689
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide HDAC5 (histone deacetylase 5) binding motif peptide: TRP-GLY-SER-GLY-GLU-VAL-LYS-LEU-ARG-LEU-GLN-GLU-PHE-LEU-LEU-SER-LYS-SER


Mass: 2080.408 Da / Num. of mol.: 1
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.: 2
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 fw: AACTATTTATAAGA


Mass: 4286.842 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: synthetic construct (others)
#4: DNA chain MADS box dsNA rev:TCTTATAAATAGTT


Mass: 4268.813 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: synthetic construct (others)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 1.79 Å3/Da
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: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.2→45.62 Å / Num. obs: 12557 / % possible obs: 100 % / Redundancy: 1.9 % / CC1/2: 0.991 / Rmerge(I) obs: 0.044 / Net I/σ(I): 9.8
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 0.306 / Num. unique obs: 1071 / CC1/2: 0.792

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→45.62 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.927 / SU B: 8.1 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.404 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26208 640 5.1 %RANDOM
Rwork0.2007 ---
obs0.20384 11879 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.122 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0 Å2-0 Å2
2---0.03 Å20 Å2
3---0.07 Å2
Refinement stepCycle: 1 / Resolution: 2.2→45.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1654 574 0 32 2260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122326
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.6943235
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.915197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.4321.61699
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.56415350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4051515
X-RAY DIFFRACTIONr_chiral_restr0.1310.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021517
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3523.846796
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.0955.737990
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.7714.521530
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined10.85350.9433604
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2555 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 52 -
Rwork0.266 853 -
obs--100 %

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