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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


eosinophil fate commitment / regulation of primitive erythrocyte differentiation / basophil differentiation / regulation of definitive erythrocyte differentiation / megakaryocyte differentiation / regulation of glycoprotein biosynthetic process / negative regulation of transcription regulatory region DNA binding / cell development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / negative regulation of bone mineralization ...eosinophil fate commitment / regulation of primitive erythrocyte differentiation / basophil differentiation / regulation of definitive erythrocyte differentiation / megakaryocyte differentiation / regulation of glycoprotein biosynthetic process / negative regulation of transcription regulatory region DNA binding / cell development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / negative regulation of bone mineralization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / dendritic cell differentiation / Factors involved in megakaryocyte development and platelet production / myeloid cell differentiation / C2H2 zinc finger domain binding / embryonic hemopoiesis / cellular response to thyroid hormone stimulus / platelet formation / positive regulation of osteoblast proliferation / transcription repressor complex / erythrocyte development / cis-regulatory region sequence-specific DNA binding / homeostasis of number of cells within a tissue / cell fate commitment / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / erythrocyte differentiation / positive regulation of erythrocyte differentiation / protein-DNA complex / chromatin DNA binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / platelet aggregation / male gonad development / cell-cell signaling / transcription regulator complex / p53 binding / sequence-specific double-stranded DNA binding / positive regulation of peptidyl-tyrosine phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / negative regulation of cell population proliferation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / positive regulation of transcription, DNA-templated / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Transcription factor GATA-1 / Transcription factor GATA / GATA-type zinc finger domain profile. / GATA-type zinc finger domain. / 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 ...Transcription factor GATA-1 / Transcription factor GATA / GATA-type zinc finger domain profile. / GATA-type zinc finger domain. / 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

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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
Water0
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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