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- PDB-6pv1: Backbone-modified variant of zinc finger 2 from the transcription... -

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Basic information

Entry
Database: PDB / ID: 6pv1
TitleBackbone-modified variant of zinc finger 2 from the transcription factor Sp1 DNA binding domain: Aib in the metal-binding turn
ComponentsTranscription factor Sp1
KeywordsDNA BINDING PROTEIN / zinc finger / proteomimetic / foldamer
Function / homology
Function and homology information


cellular response to wortmannin / positive regulation of hydrogen sulfide biosynthetic process / Regulation of CDH11 gene transcription / cellular response to zinc ion starvation / bHLH transcription factor binding / host-mediated activation of viral transcription / TGFBR3 expression / positive regulation of vascular endothelial cell proliferation / response to hydroperoxide / NFE2L2 regulating tumorigenic genes ...cellular response to wortmannin / positive regulation of hydrogen sulfide biosynthetic process / Regulation of CDH11 gene transcription / cellular response to zinc ion starvation / bHLH transcription factor binding / host-mediated activation of viral transcription / TGFBR3 expression / positive regulation of vascular endothelial cell proliferation / response to hydroperoxide / NFE2L2 regulating tumorigenic genes / positive regulation of amyloid-beta formation / histone acetyltransferase binding / 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) / positive regulation of apoptotic signaling pathway / transcription coregulator binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / euchromatin / PPARA activates gene expression / protein-DNA complex / Oncogene Induced Senescence / 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 / molecular adaptor activity / Estrogen-dependent gene expression / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / 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 / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / identical protein 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 / simulated annealing
AuthorsRao, S.R. / Horne, W.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM107161 United States
CitationJournal: Pept Sci (Hoboken) / Year: 2020
Title: Proteomimetic Zinc Finger Domains with Modified Metal-binding beta-Turns.
Authors: Rao, S.R. / Horne, W.S.
History
DepositionJul 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Derived calculations / Category: citation / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3Nov 15, 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)3,7912
Polymers3,7251
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Transcription factor Sp1


Mass: 3725.295 Da / Num. of mol.: 1
Fragment: DNA-binding domain, zinc finger 2 residues 654-684
Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P08047
#2: Chemical ChemComp-ZN / ZINC ION


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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H COSY
131isotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: 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
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMzinc finger 2 from transcription factor Sp1 DNA-binding domain, Aib turn variantnatural abundance1
10 mMTRIS[U-2H]1
0.05 mMDSSnatural abundance1
1.8 mMzinc chloridenatural abundance1
Sample conditionsIonic strength: 10 mM / Label: conditions_1 / pH: 6 pH* / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
SparkyGoddarddata analysis
ARIALinge, O'Donoghue and Nilgesrefinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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