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- PDB-1egw: CRYSTAL STRUCTURE OF MEF2A CORE BOUND TO DNA -

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Basic information

Entry
Database: PDB / ID: 1egw
TitleCRYSTAL STRUCTURE OF MEF2A CORE BOUND TO DNA
Components
  • DNA (5'-D(*AP*AP*AP*GP*CP*TP*AP*TP*TP*AP*TP*TP*AP*GP*CP*TP*T)-3')
  • DNA (5'-D(*TP*AP*AP*GP*CP*TP*AP*AP*TP*AP*AP*TP*AP*GP*CP*TP*T)-3')
  • MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A
KeywordsTRANSCRIPTION/DNA / MADS-box transcription factor / DNA-protein complex / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


ERK5 cascade / ventricular cardiac myofibril assembly / mitochondrion distribution / cardiac conduction / mitochondrial genome maintenance / dendrite morphogenesis / muscle organ development / histone acetyltransferase binding / Myogenesis / positive regulation of cardiac muscle hypertrophy ...ERK5 cascade / ventricular cardiac myofibril assembly / mitochondrion distribution / cardiac conduction / mitochondrial genome maintenance / dendrite morphogenesis / muscle organ development / histone acetyltransferase binding / Myogenesis / positive regulation of cardiac muscle hypertrophy / SMAD binding / ERK/MAPK targets / cellular response to calcium ion / positive regulation of glucose import / RNA polymerase II transcription regulatory region sequence-specific DNA binding / histone deacetylase binding / MAPK cascade / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / DNA-templated transcription / apoptotic process / chromatin binding / chromatin / positive regulation of gene expression / protein kinase binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
Similarity search - Function
SRF-like / Transcription factor, MADS-box / 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. ...SRF-like / Transcription factor, MADS-box / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Myocyte-specific enhancer factor 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, heavy atom phases from iodine derivative dataset / Resolution: 1.5 Å
AuthorsSantelli, E. / Richmond, T.J.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Crystal structure of MEF2A core bound to DNA at 1.5 A resolution.
Authors: Santelli, E. / Richmond, T.J.
History
DepositionFeb 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: DNA (5'-D(*AP*AP*AP*GP*CP*TP*AP*TP*TP*AP*TP*TP*AP*GP*CP*TP*T)-3')
F: DNA (5'-D(*TP*AP*AP*GP*CP*TP*AP*AP*TP*AP*AP*TP*AP*GP*CP*TP*T)-3')
G: DNA (5'-D(*TP*AP*AP*GP*CP*TP*AP*AP*TP*AP*AP*TP*AP*GP*CP*TP*T)-3')
H: DNA (5'-D(*AP*AP*AP*GP*CP*TP*AP*TP*TP*AP*TP*TP*AP*GP*CP*TP*T)-3')
A: MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A
B: MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A
C: MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A
D: MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A


Theoretical massNumber of molelcules
Total (without water)57,4428
Polymers57,4428
Non-polymers00
Water11,818656
1
E: DNA (5'-D(*AP*AP*AP*GP*CP*TP*AP*TP*TP*AP*TP*TP*AP*GP*CP*TP*T)-3')
F: DNA (5'-D(*TP*AP*AP*GP*CP*TP*AP*AP*TP*AP*AP*TP*AP*GP*CP*TP*T)-3')
A: MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A
B: MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A


Theoretical massNumber of molelcules
Total (without water)28,7214
Polymers28,7214
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: DNA (5'-D(*TP*AP*AP*GP*CP*TP*AP*AP*TP*AP*AP*TP*AP*GP*CP*TP*T)-3')
H: DNA (5'-D(*AP*AP*AP*GP*CP*TP*AP*TP*TP*AP*TP*TP*AP*GP*CP*TP*T)-3')
C: MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A
D: MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A


Theoretical massNumber of molelcules
Total (without water)28,7214
Polymers28,7214
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.371, 60.696, 63.987
Angle α, β, γ (deg.)115.18, 89.99, 90.00
Int Tables number1
Cell settingtriclinic
Space group name H-MP1
DetailsA protein dimer bound to a double stranded DNA oligonucleotide fully described by the deposited coordinates

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Components

#1: DNA chain DNA (5'-D(*AP*AP*AP*GP*CP*TP*AP*TP*TP*AP*TP*TP*AP*GP*CP*TP*T)-3')


Mass: 5200.408 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Consensus DNA binding site for MEF2
#2: DNA chain DNA (5'-D(*TP*AP*AP*GP*CP*TP*AP*AP*TP*AP*AP*TP*AP*GP*CP*TP*T)-3')


Mass: 5209.422 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Consensus DNA binding site for MEF2
#3: Protein
MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A / MEF2A TRANSCRIPTION FACTOR / MYOCYTE ENHANCER FACTOR 2A / MYOCYTE-SPECIFIC ENHANCER FACTOR 2A / ...MEF2A TRANSCRIPTION FACTOR / MYOCYTE ENHANCER FACTOR 2A / MYOCYTE-SPECIFIC ENHANCER FACTOR 2A / SERUM RESPONSE FACTOR-LIKE PROTEIN 1


Mass: 9155.646 Da / Num. of mol.: 4 / Fragment: N-TERMINUS, RESIDUES 2-78
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: HEART, SKELETAL MUSCLE / Production host: Escherichia coli (E. coli) / References: UniProt: Q02078
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 656 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: PEG 6000, NaCl, Ba(NO3)2, sodium Acetate, Bis-tris buffer, DTT, VAPOR DIFFUSION, HANGING DROP, temperature 295K
PH range: 5.8-6.3
Components of the solutions
IDNameCrystal-IDSol-ID
1NaClSodium chloride11
2Ba(NO3)211
3sodium Acetate11
4bis-tris buffer11
5DTT11
6PEG 600011
7PEG 600012
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115-18 %PEG60001reservoir
250 mM1reservoirNaNO3
35 mM1reservoirBa(NO3)2
450 mMBis-Tris1reservoir
525 mM1reservoirNaOAc
62 mMdithiothreitol1reservoir
71

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 0.932
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 18, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.932 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 87264 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 12.8
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.104 / % possible all: 92
Reflection shell
*PLUS
% possible obs: 92 %

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Processing

Software
NameVersionClassification
AMoREphasing
MLPHAREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, heavy atom phases from iodine derivative dataset
Resolution: 1.5→20 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1092727.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: refined also with REFMAC by Murshudov, Vagin, Dodson
RfactorNum. reflection% reflectionSelection details
Rfree0.229 8679 10 %RANDOM, CREATED IN P21
Rwork0.206 ---
obs-86651 96 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.92 Å2 / ksol: 0.316 e/Å3
Displacement parametersBiso mean: 24.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2--0.18 Å2-8.25 Å2
3----0.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2576 2764 0 656 5996
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d19.8
X-RAY DIFFRACTIONc_improper_angle_d1.46
X-RAY DIFFRACTIONc_mcbond_it1.162
X-RAY DIFFRACTIONc_mcangle_it1.853
X-RAY DIFFRACTIONc_scbond_it1.763
X-RAY DIFFRACTIONc_scangle_it2.674
LS refinement shellResolution: 1.5→1.57 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.286 1067 10.2 %
Rwork0.257 9391 -
obs--92.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.46
X-RAY DIFFRACTIONc_mcbond_it2
X-RAY DIFFRACTIONc_scbond_it3
X-RAY DIFFRACTIONc_mcangle_it3
X-RAY DIFFRACTIONc_scangle_it4
LS refinement shell
*PLUS
Rfactor Rfree: 0.286 / % reflection Rfree: 10.2 % / Rfactor Rwork: 0.257 / Rfactor obs: 0.257

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