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- PDB-1va1: Solution Structure of Transcription Factor Sp1 DNA Binding Domain... -

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Basic information

Entry
Database: PDB / ID: 1va1
TitleSolution Structure of Transcription Factor Sp1 DNA Binding Domain (Zinc Finger 1)
ComponentsTranscription factor Sp1
KeywordsTRANSCRIPTION / C2H2 type Zinc finger / Transcription Factor / DNA-Binding Protein
Function / homology
Function and homology information


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 / histone acetyltransferase binding / NFE2L2 regulating tumorigenic genes ...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 / histone acetyltransferase binding / NFE2L2 regulating tumorigenic genes / 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 / rhythmic process / sequence-specific double-stranded DNA binding / 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 / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / 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 / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Transcription factor Sp1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model type detailsminimized average
AuthorsOka, S. / Shiraishi, Y. / Yoshida, T. / Ohkubo, T. / Sugiura, Y. / Kobayashi, Y.
CitationJournal: Biochemistry / Year: 2004
Title: NMR structure of transcription factor Sp1 DNA binding domain
Authors: Oka, S. / Shiraishi, Y. / Yoshida, T. / Ohkubo, T. / Sugiura, Y. / Kobayashi, Y.
History
DepositionFeb 7, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription factor Sp1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,3732
Polymers4,3081
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)31 / 100structures with the lowest energy
RepresentativeModel #31minimized average structure

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Components

#1: Protein/peptide Transcription factor Sp1


Mass: 4308.053 Da / Num. of mol.: 1 / Fragment: Zinc finger 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SP1 / Plasmid: pEVSp1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P08047
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 1mM Sp1 DNA-Binding Domain U-15N/13C; 10mM Tris-d; 50mM NaCl; 1mM DTT
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 10mM Tris-d, 50mM NaCl / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1structure solution
NMRPipe2.1F. Delaglio, et al.processing
NMRView5.0.4Bruce A. Johnsondata analysis
CNS1.1refinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 31

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