+Open data
-Basic information
Entry | Database: PDB / ID: 2md5 | ||||||
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Title | Structure of uninhibited ETV6 ETS domain | ||||||
Components | Transcription factor ETV6 | ||||||
Keywords | TRANSCRIPTION / Protein / Auto-inhibition | ||||||
Function / homology | Function and homology information mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / neurogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / neurogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / 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 domain specific binding / regulation of DNA-templated transcription / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Model details | closest to the average, model6 | ||||||
Authors | De, S. / Mcintosh, L.P. / Chan, A.C. / Coyne, H.J. / Okon, M. / Graves, B.J. / Murphy, M.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2014 Title: Steric Mechanism of Auto-Inhibitory Regulation of Specific and Non-Specific DNA Binding by the ETS Transcriptional Repressor ETV6. Authors: De, S. / Chan, A.C. / Coyne, H.J. / Bhachech, N. / Hermsdorf, U. / Okon, M. / Murphy, M.E. / Graves, B.J. / McIntosh, L.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2md5.cif.gz | 395.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2md5.ent.gz | 335.8 KB | Display | PDB format |
PDBx/mmJSON format | 2md5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/md/2md5 ftp://data.pdbj.org/pub/pdb/validation_reports/md/2md5 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 12450.353 Da / Num. of mol.: 1 / Fragment: unp residues 329-426 / Mutation: C334S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Etv6, Tel, Tel1 / Production host: Escherichia coli (E. coli) / References: UniProt: P97360 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.6 mM [U-99% 13C; U-99% 15N] protein, 0.02 mM sodium phosphate, 0.05 mM sodium chloride, 93% H2O/7% D2O Solvent system: 93% H2O/7% D2O | ||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.11 / pH: 6.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | |||||||||||||||||||||
NMR constraints | NOE constraints total: 1655 / NOE long range total count: 472 / NOE medium range total count: 315 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 85 / Protein psi angle constraints total count: 88 | |||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | |||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 10 |