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- PDB-8tho: Solution structure of the zinc finger repeat domain of BCL11A (ZnF456) -

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Basic information

Entry
Database: PDB / ID: 8tho
TitleSolution structure of the zinc finger repeat domain of BCL11A (ZnF456)
ComponentsB-cell lymphoma/leukemia 11A
KeywordsTRANSCRIPTION / Transcription factor / zinc finger
Function / homology
Function and homology information


negative regulation of neuron remodeling / negative regulation of branching morphogenesis of a nerve / transcription regulatory region nucleic acid binding / 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 / positive regulation of collateral sprouting ...negative regulation of neuron remodeling / negative regulation of branching morphogenesis of a nerve / transcription regulatory region nucleic acid binding / 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 / positive regulation of collateral sprouting / cellular response to L-glutamate / ALK mutants bind TKIs / paraspeckles / SWI/SNF complex / protein sumoylation / transcription coregulator activity / positive regulation of neuron projection development / DNA-binding transcription repressor activity, RNA polymerase II-specific / nuclear matrix / Signaling by ALK fusions and activated point mutants / negative regulation of neuron projection development / DNA-binding transcription factor binding / postsynapse / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / 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 / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / : / C2H2 zinc finger / 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 / molecular dynamics
AuthorsViennet, T. / Yin, M. / Orkin, S.H. / Arthanari, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)EB002026 United States
CitationJournal: Structure / Year: 2024
Title: Structural insights into the DNA-binding mechanism of BCL11A: The integral role of ZnF6.
Authors: Viennet, T. / Yin, M. / Jayaraj, A. / Kim, W. / Sun, Z.J. / Fujiwara, Y. / Zhang, K. / Seruggia, D. / Seo, H.S. / Dhe-Paganon, S. / Orkin, S.H. / Arthanari, H.
History
DepositionJul 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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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)11,9004
Polymers11,7031
Non-polymers1963
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 / 20all calculated structures submitted
RepresentativeModel #1target function

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Components

#1: Protein 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: 11703.447 Da / Num. of mol.: 1 / Fragment: residues 737-835
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL11A, CTIP1, EVI9, KIAA1809, ZNF856 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H165
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D 1H-13C NOESY aliphatic
151isotropic13D 1H-13C NOESY aromatic
161isotropic13D 1H-15N NOESY

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Sample preparation

DetailsType: solution
Contents: 137 mM sodium chloride, 2.7 mM potassium chloride, 10 mM sodium phosphate, 1.8 mM potassium phosphate, 1 mM dithiothreitol, 90% H2O/10% D2O
Label: 15N_13C_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
137 mMsodium chloridenatural abundance1
2.7 mMpotassium chloridenatural abundance1
10 mMsodium phosphatenatural abundance1
1.8 mMpotassium phosphatenatural abundance1
1 mMdithiothreitolnatural abundance1
Sample conditionsIonic strength: 163 mM / Label: Sample_condition / pH: 6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospincollection
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CcpNmr Analysis2.4.2CCPNchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
RefinementMethod: molecular dynamics / Software ordinal: 5
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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