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- PDB-8q9n: Crystal Structure of the MADS-box/MEF2 Domain of MEF2D bound to d... -

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Basic information

Entry
Database: PDB / ID: 8q9n
TitleCrystal Structure of the MADS-box/MEF2 Domain of MEF2D bound to dsDNA and MITR deacetylase binding motif mutant L151V.
Components
  • (DNA MADS box) x 2
  • MEF2D protein
  • myocyte enhancer-binding factor 2-interacting transcriptional repressor (MITR or HDAC9) L151V mutant peptide: GLU-VAL-LYS-GLN-LYS-LEU-GLN-GLU-PHE-VAL-LEU-SER-LYS
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: 1.51 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 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MEF2D protein
B: MEF2D protein
K: DNA MADS box
L: DNA MADS box
X: myocyte enhancer-binding factor 2-interacting transcriptional repressor (MITR or HDAC9) L151V mutant peptide: GLU-VAL-LYS-GLN-LYS-LEU-GLN-GLU-PHE-VAL-LEU-SER-LYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2216
Polymers33,1435
Non-polymers781
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, EMSA assay
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12400 Å2
ΔGint-74 kcal/mol
Surface area14710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.326, 57.000, 76.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 2 types, 2 molecules KL

#2: DNA chain DNA MADS box


Mass: 4286.842 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA MADS box


Mass: 4268.813 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Protein / Protein/peptide , 2 types, 3 molecules ABX

#1: 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
#4: Protein/peptide myocyte enhancer-binding factor 2-interacting transcriptional repressor (MITR or HDAC9) L151V mutant peptide: GLU-VAL-LYS-GLN-LYS-LEU-GLN-GLU-PHE-VAL-LEU-SER-LYS


Mass: 2079.375 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Missing residues are not visible in the electron density maps
Source: (synth.) Homo sapiens (human)

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Non-polymers , 2 types, 150 molecules

#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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 / Density % sol: 31.39 %
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: 0.8731 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.51→45.8 Å / Num. obs: 36328 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Net I/σ(I): 12.7
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.861 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1562 / CC1/2: 0.752

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
PDB-REDOrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→45.76 Å / SU B: 1.857 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.096 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24013 1772 4.7 %RANDOM
Rwork0.19004 ---
obs0.19217 36328 99.97 %-
Displacement parametersBiso mean: 26.105 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0.04 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.51→45.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1672 574 7 149 2402

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