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- PDB-1c7u: Complex of the DNA binding core domain of the transcription facto... -

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Basic information

Entry
Database: PDB / ID: 1c7u
TitleComplex of the DNA binding core domain of the transcription factor MEF2A with a 20mer oligonucleotide
Components
  • 5'-D(*CP*TP*CP*GP*GP*CP*TP*AP*TP*TP*AP*AP*TP*AP*GP*CP*CP*GP*AP*G)-3'
  • MYOCYTE-SPECIFIC ENHANCER FACTOR 2A, C4 FORM
KeywordsTRANSCRIPTION/DNA / DNA BINDING PROTEIN / TRANSCRIPTION FACTOR / MADS-BOX / SAM DOMAIN / 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)
MethodSOLUTION NMR / simulated annealing
AuthorsClore, G.M. / Huang, K.
CitationJournal: Embo J. / Year: 2000
Title: Solution structure of the MEF2A-DNA complex: structural basis for the modulation of DNA bending and specificity by MADS-box transcription factors
Authors: Huang, K. / Louis, J.M. / Donaldson, L. / Lim, F.L. / Sharrocks, A.D. / Clore, G.M.
History
DepositionMar 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*CP*TP*CP*GP*GP*CP*TP*AP*TP*TP*AP*AP*TP*AP*GP*CP*CP*GP*AP*G)-3'
D: 5'-D(*CP*TP*CP*GP*GP*CP*TP*AP*TP*TP*AP*AP*TP*AP*GP*CP*CP*GP*AP*G)-3'
A: MYOCYTE-SPECIFIC ENHANCER FACTOR 2A, C4 FORM
B: MYOCYTE-SPECIFIC ENHANCER FACTOR 2A, C4 FORM


Theoretical massNumber of molelcules
Total (without water)32,2834
Polymers32,2834
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 35REGULARIZED MEAN STRUCTURE
Representative

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Components

#1: DNA chain 5'-D(*CP*TP*CP*GP*GP*CP*TP*AP*TP*TP*AP*AP*TP*AP*GP*CP*CP*GP*AP*G)-3'


Mass: 6133.979 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein MYOCYTE-SPECIFIC ENHANCER FACTOR 2A, C4 FORM / TRANSCRIPTION FACTOR MEF2A


Mass: 10007.484 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-86
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): BE23 / References: UniProt: Q02078

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: (1) TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN. (2) QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS. (3) 3D AND 4D HETERONUCLEAR SEPARATED AND FILTERED NOE EXPTS. (4) 2D 12C-FILTERED ...Type: (1) TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN. (2) QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS. (3) 3D AND 4D HETERONUCLEAR SEPARATED AND FILTERED NOE EXPTS. (4) 2D 12C-FILTERED EXPERIMENTS FOR DNA ASSIGNMENTS. (5) IPAP EXPTS FOR DIPOLAR COUPLINGS DIPOLAR COUPLINGS WERE MEASURED IN A BICELLE LIQUID CRYSTALLINE MEDIUM.
NMR detailsText: SOLVED BY MULTI HETERONUCLEAR NMR AND IS BASED ON 4560 EXPERIMENTAL NMR RESTRAINTS (I.E. 2280 UNIQUE ONES SINCE PROTEIN IS A HOMODIMER AND DNA IS PALINDROMIC). NOE RESTRAINTS: (A) PROTEIN: 664 ...Text: SOLVED BY MULTI HETERONUCLEAR NMR AND IS BASED ON 4560 EXPERIMENTAL NMR RESTRAINTS (I.E. 2280 UNIQUE ONES SINCE PROTEIN IS A HOMODIMER AND DNA IS PALINDROMIC). NOE RESTRAINTS: (A) PROTEIN: 664 SEQUENTIAL, 504 MEDIUM RANGE, 212 LONG RANGE, 616 INTRARESIDUE, 174 INTERSUBUNIT. (B) DNA: 428 INTRARESIDUE, 196 SEQUENTIAL INTRASTRAND, 24 INTERSTRAND. (C) PROTEIN- DNA 168. H-BOND RESTRAINTS: PROTEIN 138, DNA 120. TORSION ANGLE RESTRAINTS: PROTEIN 480 (142 PHI, 142 PSI, 112 CHI1, 68 CHI2, 16 CHI3), DNA 228. THREE-BOND HN-HALPHA COUPLING CONSTANTS: 72. SECONDARY 13C SHIFTS: 140 13CALPHA, 140 13CBETA. DIPOLAR COUPLINGS: 1DNH PROTEIN: 70, 1DCH DNA 70. REPULSIVE RESTRAINTS: 106

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Sample preparation

Sample conditionspH: 6.6 / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002
Bruker DMXBrukerDMX7503

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Processing

NMR software
NameDeveloperClassification
X-PLOR/CNSBRUNGER,ADAMS, CLORE, DELANO, GROS, GROSSE-KUNSTLEVE, JIANG, KUSZEWSKI, NILGES, PANNU, READ, RICE WARRENrefinement
CNS/X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129-136 USING THE PROGRAM XPLOR/CNS MODIFIED TO INCORPORATE COUPLING CONSTANT ...Details: THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129-136 USING THE PROGRAM XPLOR/CNS MODIFIED TO INCORPORATE COUPLING CONSTANT RESTRAINTS (GARRETT ET AL. (1984) J. MAGN. RESON. SERIES B 104, 99-103), CARBON CHEMICAL SHIFT RESTRAINTS, (KUSZEWSKI ET AL. (1995) J. MAGN. RESON. SERIES B 106, 92-96) RESTRAINTS, RESIDUAL DIPOLAR COUPLING RESTRAINTS (CLORE ET AL. J. MAGN. RESON 131, 159-162 (1998); J. MAGN 133, 216-221 (1998)), AND A CONFORMATIONAL DATABASE POTENTIAL FOR PROTEINS AND NUCLEIC ACIDS (KUSZEWSKI ET AL. PROTEIN SCI. 5, 1067-1080 (1996); J. MAGN. RESON 125, 171-177 (1997)). IN THIS ENTRY THE LAST NUMERICAL COLUMN IS THE RMS OF THE 35 INDIVIDUAL SIMULATED ANNEALING STRUCTURES ABOUT THE MEAN COORDINATE POSITIONS. THE LATTER ARE OBTAINED BY TAKING THE AVERAGE OF THE 35 SIMULATED ANNEALING STRUCTURES BEST-FITTED TO RESIDUES 1-73 AND 101-173 OF THE PROTEIN AND RESIDUES 201-240 OF THE DNA. RESIDUES 74-85 AND 174-185 ARE DISORDERED IN SOLUTION AND ARE THEREFORE NOT INCLUDED IN THE COORDINATES. THE RESTRAINED MINIMIZED MEAN STRUCTURE IS OBTAINED BY RESTRAINED REGULARIZATION OF THE AVERAGE COORDINATES AGAINST THE SAME TARGET FUNCTION USED TO CALCULATE THE SIMULATED ANNEALING STRUCTURES.
NMR ensembleConformer selection criteria: REGULARIZED MEAN STRUCTURE / Conformers calculated total number: 35 / Conformers submitted total number: 1

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