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- PDB-6byy: MEF2 CHIMERA/DNA Complex -

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Basic information

Entry
Database: PDB / ID: 6byy
TitleMEF2 CHIMERA/DNA 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*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*TP*T)-3')
  • MEF2 CHIMERA
KeywordsTRANSCRIPTION/DNA / MEF2A MEF2B MEF2 Chimera / TRANSCRIPTION / 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 / RNA polymerase II transcription regulatory region sequence-specific DNA binding / positive regulation of glucose import / histone deacetylase binding / MAPK cascade / sequence-specific double-stranded DNA binding / cell junction / 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 / protein dimerization activity / 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
Chem-1PG / 3,3',3''-phosphanetriyltripropanoic acid / DNA / DNA (> 10) / Myocyte-specific enhancer factor 2A / Myocyte-specific enhancer factor 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLei, X. / Chen, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: J. Mol. Biol. / Year: 2018
Title: The Cancer Mutation D83V Induces an alpha-Helix to beta-Strand Conformation Switch in MEF2B.
Authors: Lei, X. / Kou, Y. / Fu, Y. / Rajashekar, N. / Shi, H. / Wu, F. / Xu, J. / Luo, Y. / Chen, L.
History
DepositionDec 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 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: MEF2 CHIMERA
B: MEF2 CHIMERA
C: MEF2 CHIMERA
D: MEF2 CHIMERA
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*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*TP*T)-3')
E: DNA (5'-D(P*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*GP*A)-3')
F: DNA (5'-D(P*TP*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,84711
Polymers63,0928
Non-polymers7553
Water3,567198
1
A: MEF2 CHIMERA
B: MEF2 CHIMERA
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*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0516
Polymers31,5464
Non-polymers5052
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11210 Å2
ΔGint-53 kcal/mol
Surface area13500 Å2
MethodPISA
2
C: MEF2 CHIMERA
D: MEF2 CHIMERA
E: DNA (5'-D(P*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*GP*A)-3')
F: DNA (5'-D(P*TP*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7965
Polymers31,5464
Non-polymers2501
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10350 Å2
ΔGint-64 kcal/mol
Surface area13430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.350, 77.760, 106.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-231-

HOH

21D-113-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
MEF2 CHIMERA / Serum response factor-like protein 1 / RSRFR2 / Serum response factor-like protein 2 / Serum ...Serum response factor-like protein 1 / RSRFR2 / Serum response factor-like protein 2 / Serum response factor-like protein 1


Mass: 11343.173 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MEF2A, MEF2, MEF2B, XMEF2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q02078, UniProt: Q02080

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DNA chain , 2 types, 4 molecules KELF

#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.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*TP*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*TP*T)-3')


Mass: 4573.006 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 201 molecules

#4: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / Polyethylene glycol


Mass: 252.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H24O6
#5: Chemical ChemComp-TCE / 3,3',3''-phosphanetriyltripropanoic acid / 3-[bis(2-carboxyethyl)phosphanyl]propanoic acid / TCEP


Mass: 250.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15O6P
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HAc pH 4.7, 150 mM NaCl, 10 mM CaCl2, 5 mM MgCl2 and 28% PEG 400

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.3→54.8547 Å / Num. obs: 29180 / % possible obs: 99.95 % / Redundancy: 10.5 % / Net I/σ(I): 19.81
Reflection shellResolution: 2.3→2.382 Å

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Processing

Software
NameVersionClassification
PHENIXdev_2926refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→54.839 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.89
RfactorNum. reflection% reflection
Rfree0.2656 1364 4.67 %
Rwork0.2134 --
obs0.2159 29179 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 141.69 Å2 / Biso mean: 51.1924 Å2 / Biso min: 15.49 Å2
Refinement stepCycle: final / Resolution: 2.3→54.839 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3012 1125 40 198 4375
Biso mean--62.2 41.89 -
Num. residues----417
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3001-2.38230.36231510.261327202871
2.3823-2.47770.33691020.23927722874
2.4777-2.59040.30491310.230927532884
2.5904-2.7270.28981210.231327442865
2.727-2.89780.28131510.241627352886
2.8978-3.12160.29211520.238727552907
3.1216-3.43570.26821250.205227742899
3.4357-3.93270.251420.20627982940
3.9327-4.95430.22311200.186328302950
4.9543-54.85470.25131690.20729343103

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