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- PDB-8vg3: Formerly degenerate seventh zinc finger domain from transcription... -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8vg3
TitleFormerly degenerate seventh zinc finger domain from transcription factor ZNF711 rehabilitated by experimental NMR structure
ComponentsZinc finger protein 711
KeywordsMETAL BINDING PROTEIN / ZNF711 / CMPX1 / XLID97 / degenerate zinc finger
Function / homology
Function and homology information


Generic Transcription Pathway / regulation of gene expression / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / metal ion binding / nucleus
Similarity search - Function
Transcriptional activator, Zfx / Zfy domain / Zfx / Zfy transcription activation region / C2H2-type zinc-finger domain / 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
Zinc finger protein 711
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsRua, A.J. / Alexandrescu, A.T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Formerly degenerate seventh zinc finger domain from transcription factor ZNF711 rehabilitated by experimental NMR structure
Authors: Rua, A.J. / Alexandrescu, A.T.
History
DepositionDec 22, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zinc finger protein 711
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,3822
Polymers3,3171
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Zinc finger protein 711 /


Mass: 3316.729 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9Y462
#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
212isotropic12D 1H-1H NOESY
222isotropic12D 1H-1H TOCSY
232isotropic12D 1H-15N SOFAST HMQC
141isotropic12D 1H-13C HSQC
252isotropic12D 1H-1H DQF-COSY
161isotropic12D 1H-1H TOCSY
171isotropic12D 1H-1H NOESY
181isotropic2DOSY
292isotropic32D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution12.4 mM Z711-7, 4.4 mM ZnSO4, 100% D2OSample for experiments and assignments in D2Osample_1100% D2O
solution22.4 mM Z711-7, 4.4 mM ZnSO4, 90% H2O/10% D2OSample used for most NMR assignments and experiments in H2Osample_290% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.4 mMZ711-7none1
4.4 mMZnSO4none1
2.4 mMZ711-7none2
4.4 mMZnSO4none2
Sample conditions

Ionic strength: 0 Not defined / PH err: 0.1 / Pressure: 1 atm

Conditions-IDDetailsLabelpHTemperature (K)
2These sample conditions were used for structure determination. The HN of Leu16 at ~11.1 ppm (which is important for assignments and structure) can only beseen clearly at the low temperature of 283 K (10 C).conditions 26.2 283 K
1Conditions for D2O sample (Sample 1)conditions 16.2 pD298 K
3Conditions for H2O sample (Sample 2) at 25 Cconditions_36.2 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE6001600 MHz MIT
Varian INOVAVarianINOVA6002600 MHz Storrs
Bruker AVANCE NEOBrukerAVANCE NEO8003800 MHz UCHC

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Processing

NMR software
NameDeveloperClassification
CcpNmr AnalysisCCPNchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 3
Details: NESG script prot_sa_refine.inp -> obtained from here: https://nesgwiki.chem.buffalo.edu/index.php/Structure_Refinement_Using_XPLOR-NIH
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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