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- PDB-3kov: Structure of MEF2A bound to DNA reveals a completely folded MADS-... -

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Basic information

Entry
Database: PDB / ID: 3kov
TitleStructure of MEF2A bound to DNA reveals a completely folded MADS-box/MEF2 domain that recognizes DNA and recruits transcription co-factors
Components
  • DNA (5'-D(*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*G)-3')
  • DNA (5'-D(*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*T)-3')
  • Myocyte-specific enhancer factor 2A
KeywordsTRANSCRIPTION/DNA / MADS-box/MEF2 domain / transcription co-factors / protein-DNA complex / protein-protein docking / Acetylation / Activator / Alternative splicing / Apoptosis / Developmental protein / Differentiation / Disease mutation / DNA-binding / Isopeptide bond / Neurogenesis / Nucleus / Phosphoprotein / Transcription / Transcription regulation / Ubl conjugation / 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 / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWu, Y. / Dey, R. / Han, A. / Jayathilaka, N. / Philips, M. / Ye, J. / Chen, L.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structure of the MADS-box/MEF2 Domain of MEF2A Bound to DNA and Its Implication for Myocardin Recruitment.
Authors: Wu, Y. / Dey, R. / Han, A. / Jayathilaka, N. / Philips, M. / Ye, J. / Chen, L.
History
DepositionNov 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 21, 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
A: Myocyte-specific enhancer factor 2A
B: Myocyte-specific enhancer factor 2A
I: Myocyte-specific enhancer factor 2A
J: Myocyte-specific enhancer factor 2A
C: DNA (5'-D(*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*G)-3')
D: DNA (5'-D(*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*T)-3')
K: DNA (5'-D(*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*G)-3')
L: DNA (5'-D(*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)58,3908
Polymers58,3908
Non-polymers00
Water0
1
A: Myocyte-specific enhancer factor 2A
B: Myocyte-specific enhancer factor 2A
C: DNA (5'-D(*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*G)-3')
D: DNA (5'-D(*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)29,1954
Polymers29,1954
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: Myocyte-specific enhancer factor 2A
J: Myocyte-specific enhancer factor 2A
K: DNA (5'-D(*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*G)-3')
L: DNA (5'-D(*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)29,1954
Polymers29,1954
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.801, 77.960, 106.794
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain I
211chain J
112chain I
212chain A
113chain I
213chain B

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Myocyte-specific enhancer factor 2A / Serum response factor-like protein 1


Mass: 10628.313 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MEF2A, MEF2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q02078
#2: DNA chain DNA (5'-D(*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*G)-3')


Mass: 3973.635 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*T)-3')


Mass: 3964.621 Da / Num. of mol.: 2 / Source method: obtained synthetically

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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: 2.77 Å3/Da / Density % sol: 55.65 %
Crystal growTemperature: 291 K / Method: hanging drop / pH: 4.7
Details: 50 mM acetic acid, 142mM NaCl, 5mM MgCl2, 10mM CaCl2, 3.3% Glycerol, 22.5% 3K PEG, pH 4.7, hanging drop, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1acetic acid11
2NaClSodium chloride11
3MgCl211
4CaCl211
5Glycerol11
63K PEG11
7acetic acid12
8NaClSodium chloride12
9MgCl212
10CaCl212
11Glycerol12
123K PEG12

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.87→50 Å / Num. obs: 15478 / % possible obs: 99.6 % / Redundancy: 7 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 30
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.87-2.976.90.58599.5
2.97-3.097.10.384100
3.09-3.237.20.223100
3.23-3.47.20.161100
3.4-3.627.20.092100
3.62-3.897.20.06999.7
3.89-4.297.10.04899.9
4.29-4.916.90.03799
4.91-6.186.90.03699.7
6.18-506.40.03498

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→44.054 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 1.37 / σ(F): 1.34 / Phase error: 27.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2786 704 5 %
Rwork0.2207 --
obs0.2238 14094 94.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.484 Å2 / ksol: 0.306 e/Å3
Displacement parametersBiso mean: 86.824 Å2
Baniso -1Baniso -2Baniso -3
1-4.286 Å20 Å20 Å2
2--8.62 Å2-0 Å2
3---16.81 Å2
Refinement stepCycle: LAST / Resolution: 2.9→44.054 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2972 1581 0 0 4553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084778
X-RAY DIFFRACTIONf_angle_d1.2276741
X-RAY DIFFRACTIONf_dihedral_angle_d24.531932
X-RAY DIFFRACTIONf_chiral_restr0.061758
X-RAY DIFFRACTIONf_plane_restr0.003586
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11I743X-RAY DIFFRACTIONPOSITIONAL
12J743X-RAY DIFFRACTIONPOSITIONAL0.048
21I743X-RAY DIFFRACTIONPOSITIONAL
22A743X-RAY DIFFRACTIONPOSITIONAL0.043
31I743X-RAY DIFFRACTIONPOSITIONAL
32B743X-RAY DIFFRACTIONPOSITIONAL0.041
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.12390.37351490.30172652X-RAY DIFFRACTION96
3.1239-3.43820.30291480.24762656X-RAY DIFFRACTION96
3.4382-3.93550.29651510.22232686X-RAY DIFFRACTION96
3.9355-4.95720.26761270.1912670X-RAY DIFFRACTION94
4.9572-44.05930.24451290.21112726X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: 22.3433 Å / Origin y: 32.0434 Å / Origin z: 80.5156 Å
111213212223313233
T0.7517 Å20.0612 Å2-0.2334 Å2-0.6428 Å20.0588 Å2--0.5708 Å2
L0.1714 °20.0448 °2-0.4187 °2-1.5541 °21.2344 °2--1.1831 °2
S-0.0895 Å °-0.0611 Å °-0.0492 Å °0.5618 Å °-0.0846 Å °-0.0046 Å °0.2893 Å °0.3341 Å °0.087 Å °
Refinement TLS groupSelection details: all

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