+Open data
-Basic information
Entry | Database: PDB / ID: 1egw | ||||||
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Title | CRYSTAL STRUCTURE OF MEF2A CORE BOUND TO DNA | ||||||
Components |
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Keywords | TRANSCRIPTION/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 / ERK/MAPK targets / SMAD binding / 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 / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA-templated transcription / apoptotic process / chromatin binding / positive regulation of gene expression / chromatin / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, heavy atom phases from iodine derivative dataset / Resolution: 1.5 Å | ||||||
Authors | Santelli, E. / Richmond, T.J. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1egw.cif.gz | 153.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1egw.ent.gz | 120.8 KB | Display | PDB format |
PDBx/mmJSON format | 1egw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1egw_validation.pdf.gz | 450.3 KB | Display | wwPDB validaton report |
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Full document | 1egw_full_validation.pdf.gz | 455.2 KB | Display | |
Data in XML | 1egw_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 1egw_validation.cif.gz | 37.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/1egw ftp://data.pdbj.org/pub/pdb/validation_reports/eg/1egw | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | A protein dimer bound to a double stranded DNA oligonucleotide fully described by the deposited coordinates |
-Components
#1: DNA chain | Mass: 5200.408 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Consensus DNA binding site for MEF2 #2: DNA chain | Mass: 5209.422 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Consensus DNA binding site for MEF2 #3: Protein | 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.84 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 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 |
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Crystal grow | *PLUS Temperature: 22 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 0.932 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 18, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.932 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 1.5→1.55 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.104 / % possible all: 92 |
Reflection shell | *PLUS % possible obs: 92 % |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.92 Å2 / ksol: 0.316 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.57 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 8
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Xplor file |
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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
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LS refinement shell | *PLUS Rfactor Rfree: 0.286 / % reflection Rfree: 10.2 % / Rfactor Rwork: 0.257 / Rfactor obs: 0.257 |