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- PDB-1znm: A zinc finger with an artificial beta-turn, original sequence tak... -

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Basic information

Entry
Database: PDB / ID: 1znm
TitleA zinc finger with an artificial beta-turn, original sequence taken from the third zinc finger domain of the human transcriptional repressor protein YY1 (YING and YANG 1, a delta transcription factor), nmr, 34 structures
ComponentsYY1
KeywordsZINC FINGER / ZN-BTD(7 / 8)-3YY1 / BETA-TURN MIMETIC / TRANSCRIPTION REGULATION
Function / homology
Function and homology information


response to prostaglandin F / RNA localization / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / negative regulation of cell growth involved in cardiac muscle cell development / PcG protein complex / camera-type eye morphogenesis / Ino80 complex / chromatin silencing complex / negative regulation of interferon-beta production ...response to prostaglandin F / RNA localization / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / negative regulation of cell growth involved in cardiac muscle cell development / PcG protein complex / camera-type eye morphogenesis / Ino80 complex / chromatin silencing complex / negative regulation of interferon-beta production / response to UV-C / anterior/posterior pattern specification / regulation of chromosome organization / DNA-binding transcription repressor activity / immunoglobulin heavy chain V-D-J recombination / SMAD binding / regulation of DNA replication / regulation of embryonic development / regulation of DNA repair / cellular response to interleukin-1 / cis-regulatory region sequence-specific DNA binding / four-way junction DNA binding / positive regulation of DNA repair / telomere maintenance / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / B cell differentiation / negative regulation of miRNA transcription / double-strand break repair via homologous recombination / DNA Damage Recognition in GG-NER / nuclear matrix / DNA-binding transcription repressor activity, RNA polymerase II-specific / Activation of anterior HOX genes in hindbrain development during early embryogenesis / UCH proteinases / cellular response to UV / sequence-specific double-stranded DNA binding / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription regulator complex / transcription cis-regulatory region binding / regulation of cell cycle / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / DNA damage response / chromatin binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
C2H2-type Zinc finger protein, YY1-like / 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
Transcriptional repressor protein YY1
Similarity search - Component
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsViles, J.H. / Patel, S.U. / Mitchell, J.B.O. / Moody, C.M. / Justice, D.E. / Uppenbrink, J. / Doyle, P.M. / Harris, C.J. / Sadler, P.J. / Thornton, J.M.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Design, synthesis and structure of a zinc finger with an artificial beta-turn.
Authors: Viles, J.H. / Patel, S.U. / Mitchell, J.B. / Moody, C.M. / Justice, D.E. / Uppenbrink, J. / Doyle, P.M. / Harris, C.J. / Sadler, P.J. / Thornton, J.M.
History
DepositionNov 20, 1997Processing site: BNL
Revision 1.0Apr 1, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YY1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,2992
Polymers3,2341
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)34 / 100NO NOE VIOLATIONS ABOVE 0.2 ANGSTROM AND 5 DEGREE DIHEDRAL ANGLE
Representative

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Components

#1: Protein/peptide YY1 / ZN-BTD(7 / 8)-3YY1


Mass: 3233.828 Da / Num. of mol.: 1 / Fragment: ZINC FINGER DNA BINDING DOMAIN 3 FROM YY1 / Source method: obtained synthetically
Details: SEQUENCE SYNTHESISED USING FMOC CHEMISTRY, WITH BETA-TURN MIMETIC BTD IN POSITIONS 7 AND 8
References: UniProt: P25490
#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
111ROESY
121NOESY
131COSY
141TOCSY

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Sample preparation

Sample conditionspH: 6.0 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX6001
Varian VXR600VarianVXR6006002

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
X-PLORstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: THE STRUCTURES WERE CALCULATED USING AN AB-INITIO SIMULATED ANNEALING PROTOCOL ESSENTIALLY AS SUPPLIED WITH X-PLOR 3.851, STARTING FROM STRUCTURES WITH RANDOMIZED PHI AND PSI ANGLES. THE ...Details: THE STRUCTURES WERE CALCULATED USING AN AB-INITIO SIMULATED ANNEALING PROTOCOL ESSENTIALLY AS SUPPLIED WITH X-PLOR 3.851, STARTING FROM STRUCTURES WITH RANDOMIZED PHI AND PSI ANGLES. THE ZINC ION WAS INCORPORATED WITH THE APPROPRIATE GEOMETRIC CONSTRAINTS TO PRODUCE TETRAHEDRAL ZINC CO-ORDINATION.
NMR ensembleConformer selection criteria: NO NOE VIOLATIONS ABOVE 0.2 ANGSTROM AND 5 DEGREE DIHEDRAL ANGLE
Conformers calculated total number: 100 / Conformers submitted total number: 34

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