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- PDB-6pv1: Backbone-modified variant of zinc finger 2 from the transcription... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6pv1 | ||||||
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Title | Backbone-modified variant of zinc finger 2 from the transcription factor Sp1 DNA binding domain: Aib in the metal-binding turn | ||||||
![]() | Transcription factor Sp1 | ||||||
![]() | DNA BINDING PROTEIN / zinc finger / proteomimetic / foldamer | ||||||
Function / homology | ![]() cellular response to wortmannin / positive regulation of hydrogen sulfide biosynthetic process / Regulation of CDH11 gene transcription / bHLH transcription factor binding / cellular response to zinc ion starvation / positive regulation by host of viral transcription / response to hydroperoxide / positive regulation of vascular endothelial cell proliferation / NFE2L2 regulating tumorigenic genes / histone acetyltransferase binding ...cellular response to wortmannin / positive regulation of hydrogen sulfide biosynthetic process / Regulation of CDH11 gene transcription / bHLH transcription factor binding / cellular response to zinc ion starvation / positive regulation by host of viral transcription / response to hydroperoxide / positive regulation of vascular endothelial cell proliferation / NFE2L2 regulating tumorigenic genes / histone acetyltransferase binding / positive regulation of amyloid-beta formation / RNA polymerase II transcribes snRNA genes / positive regulation of blood vessel endothelial cell migration / cellular response to estrogen stimulus / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / transcription repressor complex / Activation of gene expression by SREBF (SREBP) / transcription coregulator binding / protein-DNA complex / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / euchromatin / Oncogene Induced Senescence / PPARA activates gene expression / histone deacetylase binding / cellular response to insulin stimulus / positive regulation of angiogenesis / sequence-specific double-stranded DNA binding / rhythmic process / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / molecular adaptor activity / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
![]() | Rao, S.R. / Horne, W.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Proteomimetic Zinc Finger Domains with Modified Metal-binding beta-Turns. Authors: Rao, S.R. / Horne, W.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.9 KB | Display | ![]() |
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PDB format | ![]() | 98.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6pv0C ![]() 6pv2C ![]() 6pv3C ![]() 6ucoC ![]() 6ucpC C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein/peptide | Mass: 3725.295 Da / Num. of mol.: 1 Fragment: DNA-binding domain, zinc finger 2 residues 654-684 Source method: obtained synthetically / Source: (synth.) ![]() |
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#2: Chemical | ChemComp-ZN / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Type: solution Contents: 1.5 mM zinc finger 2 from transcription factor Sp1 DNA-binding domain, Aib turn variant, 10 mM [U-2H] TRIS, 0.05 mM DSS, 1.8 mM zinc chloride, 90% H2O/10% D2O Label: sample_1 / Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 10 mM / Label: conditions_1 / pH: 6 pH* / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 3 | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 10 |