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- PDB-1gnf: SOLUTION STRUCTURE OF THE N-TERMINAL ZINC FINGER OF MURINE GATA-1... -

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Basic information

Entry
Database: PDB / ID: 1gnf
TitleSOLUTION STRUCTURE OF THE N-TERMINAL ZINC FINGER OF MURINE GATA-1, NMR, 25 STRUCTURES
ComponentsTRANSCRIPTION FACTOR GATA-1
KeywordsTRANSCRIPTION REGULATION / ZINC FINGER
Function / homology
Function and homology information


regulation of primitive erythrocyte differentiation / basophil differentiation / eosinophil fate commitment / regulation of definitive erythrocyte differentiation / regulation of glycoprotein biosynthetic process / megakaryocyte differentiation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / cell development / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Sertoli cell development ...regulation of primitive erythrocyte differentiation / basophil differentiation / eosinophil fate commitment / regulation of definitive erythrocyte differentiation / regulation of glycoprotein biosynthetic process / megakaryocyte differentiation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / cell development / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Sertoli cell development / dendritic cell differentiation / Factors involved in megakaryocyte development and platelet production / negative regulation of bone mineralization / positive regulation of mast cell degranulation / cellular response to follicle-stimulating hormone stimulus / myeloid cell differentiation / C2H2 zinc finger domain binding / embryonic hemopoiesis / platelet formation / DNA binding, bending / positive regulation of osteoblast proliferation / animal organ regeneration / cell fate commitment / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / cis-regulatory region sequence-specific DNA binding / erythrocyte development / transcription repressor complex / homeostasis of number of cells within a tissue / positive regulation of erythrocyte differentiation / cellular response to cAMP / transcription coregulator binding / erythrocyte differentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / protein-DNA complex / chromatin DNA binding / platelet aggregation / male gonad development / transcription coactivator binding / sequence-specific double-stranded DNA binding / p53 binding / cell-cell signaling / positive regulation of cytosolic calcium ion concentration / cellular response to lipopolysaccharide / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA binding / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / chromatin binding / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
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 / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Zinc finger, NHR/GATA-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Erythroid transcription factor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsKowalski, K. / Czolij, R. / King, G.F. / Crossley, M. / Mackay, J.P.
CitationJournal: J.Biomol.NMR / Year: 1999
Title: The solution structure of the N-terminal zinc finger of GATA-1 reveals a specific binding face for the transcriptional co-factor FOG.
Authors: Kowalski, K. / Czolij, R. / King, G.F. / Crossley, M. / Mackay, J.P.
History
DepositionOct 12, 1998Processing site: BNL
Revision 1.0Jun 8, 1999Provider: 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
Revision 1.4May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSCRIPTION FACTOR GATA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2652
Polymers5,2001
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 1000LOWEST RESIDUAL RESTRAINT VIOLATIONS
Representative

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Components

#1: Protein/peptide TRANSCRIPTION FACTOR GATA-1


Mass: 5199.939 Da / Num. of mol.: 1 / Fragment: N-TERMINAL ZINC FINGER
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: BL21 / Plasmid: PGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P17679
#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
111TOCSY
121DQFCOSY
131NOESY
141ECOSY
151HSQC
161TOCSY-HSQC
171NOESY-HSQC
181J-MODULATED HMQC
NMR detailsText: THE STRUCTURE WAS DETERMINED USING HOMONUCLEAR 1H, AND HETERONUCLEAR 1H/15N NMR SPECTROSCOPY

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Sample preparation

DetailsContents: 95% H2O:5% D2O
Sample conditionspH: 5.4 / Pressure: 1 atm / Temperature: 288 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMX600BrukerAMX6006001
Bruker DRX500BrukerDRX5006002

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Processing

Software
NameVersionClassification
X-PLOR3.843model building
X-PLOR3.843refinement
X-PLOR3.843phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.843BRUNGERrefinement
DIANA2.12structure solution
X-PLOR3.843structure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: LOWEST RESIDUAL RESTRAINT VIOLATIONS
Conformers calculated total number: 1000 / Conformers submitted total number: 25

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