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- PDB-5ion: Solution Structure of Miz-1 Zinc Finger 13 -

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Basic information

Entry
Database: PDB / ID: 5ion
TitleSolution Structure of Miz-1 Zinc Finger 13
ComponentsZinc finger and BTB domain-containing protein 17
KeywordsTRANSCRIPTION / C2H2 Zinc finger / Miz-1 / ZBTB17 / transcription factor
Function / homology
Function and homology information


ectoderm development / XBP1(S) activates chaperone genes / regulation of immune system process / gastrulation with mouth forming second / G1 to G0 transition / negative regulation of cell cycle / core promoter sequence-specific DNA binding / regulation of cytokine production / protein-DNA complex / transcription coactivator binding ...ectoderm development / XBP1(S) activates chaperone genes / regulation of immune system process / gastrulation with mouth forming second / G1 to G0 transition / negative regulation of cell cycle / core promoter sequence-specific DNA binding / regulation of cytokine production / protein-DNA complex / transcription coactivator binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / metal ion binding
Similarity search - Function
C2H2-type zinc finger / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / SKP1/BTB/POZ domain superfamily ...C2H2-type zinc finger / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Zinc finger and BTB domain-containing protein 17
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsTremblay, C. / Bedard, M. / Lavigne, P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2016
Title: Solution structure of the 13th C2H2 Zinc Finger of Miz-1.
Authors: Tremblay, C. / Bedard, M. / Bonin, M.A. / Lavigne, P.
History
DepositionMar 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2May 4, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Structure summary
Category: citation / entity / pdbx_audit_support
Item: _citation.journal_id_CSD / _entity.pdbx_number_of_molecules / _pdbx_audit_support.funding_organization
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_software
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name
Revision 1.5Jun 14, 2023Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_conn.pdbx_dist_value
Revision 1.6May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Zinc finger and BTB domain-containing protein 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,2982
Polymers3,2331
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 300structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Zinc finger and BTB domain-containing protein 17 / Myc-interacting zinc finger protein 1 / Miz-1 / Zinc finger protein 151 / Zinc finger protein 60


Mass: 3232.629 Da / Num. of mol.: 1 / Fragment: UNP residues 714-742 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13105
#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-IDSample stateSpectrometer-IDType
112isotropic12D 1H-1H NOESY
122isotropic12D 1H-1H TOCSY
132isotropic12D 1H-13C HSQC aliphatic
142isotropic12D 1H-13C HSQC aromatic
152isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution / Contents: 0.75 mM 1H ZF 13, 90% H2O/10% D2O / Label: ZF13 sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.75 mM / Component: ZF 13 / Isotopic labeling: 1H
Sample conditionsIonic strength: 0.05 M / Label: C1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian Unity Inova / Manufacturer: Varian / Model: Unity Inova / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe7.4Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNchemical shift assignment
DANGLE1.1CCPNdata analysis
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readrefinement
ARIA2.2Linge, O'Donoghue and Nilgesstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 20

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