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- PDB-9bv0: NMR structure of the Z0 CCHC zinc-finger of transcription repress... -

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Basic information

Entry
Database: PDB / ID: 9bv0
TitleNMR structure of the Z0 CCHC zinc-finger of transcription repressor Bcl11A
ComponentsB-cell lymphoma/leukemia 11A
KeywordsMETAL BINDING PROTEIN / C2HC zinc finger / atypical zinc finger / protein interacting zinc finger / FOG-related / Bcl11A / transcription repressor
Function / homology
Function and homology information


negative regulation of neuron remodeling / transcription regulatory region nucleic acid binding / negative regulation of branching morphogenesis of a nerve / negative regulation of dendrite extension / negative regulation of protein homooligomerization / negative regulation of collateral sprouting / regulation of dendrite development / negative regulation of dendrite development / negative regulation of axon extension / cellular response to L-glutamate ...negative regulation of neuron remodeling / transcription regulatory region nucleic acid binding / negative regulation of branching morphogenesis of a nerve / negative regulation of dendrite extension / negative regulation of protein homooligomerization / negative regulation of collateral sprouting / regulation of dendrite development / negative regulation of dendrite development / negative regulation of axon extension / cellular response to L-glutamate / positive regulation of collateral sprouting / paraspeckles / ALK mutants bind TKIs / SWI/SNF complex / protein sumoylation / transcription coregulator activity / Signaling by ALK fusions and activated point mutants / DNA-binding transcription repressor activity, RNA polymerase II-specific / nuclear matrix / positive regulation of neuron projection development / negative regulation of neuron projection development / postsynapse / DNA-binding transcription factor binding / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of gene expression / regulation of transcription by RNA polymerase II / protein kinase binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / cytosol / 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
B-cell lymphoma/leukemia 11A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsAlexandrescu, A.T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: NMR structure of the Z0 CCHC zinc-finger of transcription repressor Bcl11A
Authors: Alexandrescu, A.T.
History
DepositionMay 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: B-cell lymphoma/leukemia 11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,2202
Polymers3,1551
Non-polymers651
Water00
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 / 60structures with the least restraint violations
RepresentativeModel #1medoid

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Components

#1: Protein/peptide B-cell lymphoma/leukemia 11A / BCL-11A / B-cell CLL/lymphoma 11A / COUP-TF-interacting protein 1 / Ecotropic viral integration ...BCL-11A / B-cell CLL/lymphoma 11A / COUP-TF-interacting protein 1 / Ecotropic viral integration site 9 protein homolog / EVI-9 / Zinc finger protein 856


Mass: 3154.750 Da / Num. of mol.: 1
Fragment: B0 atypical C2HC zinc-finger domain, residues 46-72
Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9H165
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
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 NOESY
121isotropic12D 1H-1H TOCSY
232isotropic12D 1H-1H NOESY
242isotropic12D 1H-1H NOESY
252isotropic12D 1H-1H TOCSY
262isotropic12D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution140 uM Bcl11A-Z0, 600 uM Zn2+, 90% H2O/10% D20H2O samplesample_190% H2O/10% D20
solution240 uM Bcl11A-Z0, 600 uM Zn2+, 100% D20D2O samplesample_2100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
40 uMBcl11A-Z0natural abundance1
600 uMZn2+natural abundance1
40 uMBcl11A-Z0natural abundance2
600 uMZn2+natural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPH errPressure (kPa)Temperature (K)
10.6 mMsample_16.3 0.11 atm298 K
20.6 mMsample_25.8 pD0.11 atm298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz / Details: cryogenic probe

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.5.2CCPNchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIH3.8Schwieters, Kuszewski, Tjandra and Clorerefinement
CcpNmr Analysis2.5.2CCPNpeak picking
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 60 / Conformers submitted total number: 20

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