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- PDB-8c84: Crystal structure of MADS-box/MEF2D N-terminal domain complex -

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Basic information

Entry
Database: PDB / ID: 8c84
TitleCrystal structure of MADS-box/MEF2D N-terminal domain complex
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')
  • MEF2D protein
KeywordsTRANSCRIPTION / transcriptional regulator
Function / homology
Function and homology information


histone deacetylase binding / heart development / cell differentiation / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionJan 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 17, 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

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Assembly

Deposited unit
A: MEF2D protein
B: MEF2D protein
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)30,6874
Polymers30,6874
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10660 Å2
ΔGint-62 kcal/mol
Surface area13670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.033, 56.364, 75.596
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 MEF2D protein / Myocyte-specific enhancer factor 2D


Mass: 11065.788 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
#2: 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.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: 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.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 1.84 Å3/Da / Density % sol: 33.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 200 mM sodium acetate trihydrate, 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: 0.9724 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.9→45.19 Å / Num. obs: 18562 / % possible obs: 99.8 % / Redundancy: 8.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.1
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.893 / Num. unique obs: 1182 / CC1/2: 0.791

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
PHENIX1.18.2refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→45.19 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.414 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25118 952 5.2 %RANDOM
Rwork0.20377 ---
obs0.20619 18412 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.396 Å2
Baniso -1Baniso -2Baniso -3
1-2.06 Å2-0 Å20 Å2
2---0.43 Å2-0 Å2
3----1.63 Å2
Refinement stepCycle: 1 / Resolution: 1.9→45.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1527 574 0 73 2174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122190
X-RAY DIFFRACTIONr_angle_refined_deg1.8821.6993054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8125181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.6521.6392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.92615324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6411514
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021419
X-RAY DIFFRACTIONr_mcbond_it2.9683.114730
X-RAY DIFFRACTIONr_mcangle_it4.0554.644909
X-RAY DIFFRACTIONr_scbond_it4.9364.1381460
X-RAY DIFFRACTIONr_long_range_B_refined9.63646.293521
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 63 -
Rwork0.272 1271 -
obs--99.78 %

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