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- PDB-6zfv: Solution NMR structure of human GATA2 N-terminal zinc finger domain -

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Basic information

Entry
Database: PDB / ID: 6zfv
TitleSolution NMR structure of human GATA2 N-terminal zinc finger domain
ComponentsEndothelial transcription factor GATA-2
KeywordsTRANSCRIPTION / GATA / Transcription factor / Haematopoeisis
Function / homology
Function and homology information


semicircular canal development / regulation of forebrain neuron differentiation / : / commitment of neuronal cell to specific neuron type in forebrain / ventral spinal cord interneuron differentiation / cell differentiation in hindbrain / regulation of primitive erythrocyte differentiation / eosinophil fate commitment / GABAergic neuron differentiation / negative regulation of fat cell proliferation ...semicircular canal development / regulation of forebrain neuron differentiation / : / commitment of neuronal cell to specific neuron type in forebrain / ventral spinal cord interneuron differentiation / cell differentiation in hindbrain / regulation of primitive erythrocyte differentiation / eosinophil fate commitment / GABAergic neuron differentiation / negative regulation of fat cell proliferation / negative regulation of macrophage differentiation / urogenital system development / glandular epithelial cell maturation / thyroid-stimulating hormone-secreting cell differentiation / negative regulation of brown fat cell differentiation / negative regulation of hematopoietic progenitor cell differentiation / negative regulation of neural precursor cell proliferation / hematopoietic stem cell homeostasis / positive regulation of megakaryocyte differentiation / vascular wound healing / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of mast cell degranulation / positive regulation of phagocytosis, engulfment / cell fate determination / C2H2 zinc finger domain binding / definitive hemopoiesis / negative regulation of neuroblast proliferation / inner ear morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / response to lipid / cochlea development / negative regulation of fat cell differentiation / negative regulation of Notch signaling pathway / central nervous system neuron development / somatic stem cell population maintenance / neuroblast proliferation / embryonic placenta development / positive regulation of blood vessel endothelial cell migration / cell fate commitment / hematopoietic progenitor cell differentiation / phagocytosis / negative regulation of endothelial cell apoptotic process / brown fat cell differentiation / positive regulation of phagocytosis / homeostasis of number of cells within a tissue / positive regulation of neuron differentiation / positive regulation of erythrocyte differentiation / transcription coregulator binding / neuron migration / transcription coactivator binding / positive regulation of miRNA transcription / Transcriptional regulation of granulopoiesis / positive regulation of angiogenesis / sequence-specific double-stranded DNA binding / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / chromatin binding / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Transcription factor, GATA-2/3 / Transcription factor GATA / GATA-type zinc finger domain. / GATA-type zinc finger domain profile. / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type / Zinc finger, NHR/GATA-type
Similarity search - Domain/homology
Endothelial transcription factor GATA-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsNurmohamed, S.S. / Broadhurst, R.W. / May, G. / Enver, T.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Kay Kendall Leukaemia Fund United Kingdom
CitationJournal: To Be Published
Title: Solution NMR structure of human GATA2 C-terminal zinc finger domain
Authors: Nurmohamed, S.S. / Broadhurst, R.W. / May, G. / Enver, T.
History
DepositionJun 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2Jun 19, 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: Endothelial transcription factor GATA-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1252
Polymers7,0601
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4760 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Endothelial transcription factor GATA-2 / GATA-binding protein 2


Mass: 7060.018 Da / Num. of mol.: 1 / Fragment: UNP residues 291-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GATA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P23769
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D 1H-15N NOESY
121isotropic23D 1H-13C NOESY
131isotropic13D HNCA
141isotropic13D HN(CA)CB
151isotropic13D CBCA(CO)NH
161isotropic13D HNCO
181isotropic13D HBHA(CO)NH
171isotropic13D 1H-15N TOCSY
1101isotropic22D 1H-15N HSQC
191isotropic22D 1H-13C HSQC

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Sample preparation

DetailsType: solution
Contents: 10.0 mg/mL [U-99% 13C; U-99% 15N] GATA2 zinc finger 1, 90% H2O/10% D2O
Details: 10mM 2-(N-morpholino)ethanesulfonic acid, 150mM Sodium Chloride, 1mM tris(2-carboxyethyl)phosphine, 0.1mM 3,3,3-Trimethylsilylpropionate
Label: 13C_15N_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 10.0 mg/mL / Component: GATA2 zinc finger 1 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 150 mM / Label: GATA_NF / pH: 5.8 / Pressure: 1 atm / Temperature: 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRX500BrukerDRX5005001
Bruker DRX800BrukerDRX8008002

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3Linge, O'Donoghue and Nilgesrefinement
CcpNmr Analysis2.4.1CCPNchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 20

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