+Open data
-Basic information
Entry | Database: PDB / ID: 2l6z | ||||||
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Title | haddock model of GATA1NF:Lmo2LIM2-Ldb1LID with FOG | ||||||
Components |
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Keywords | Transcription regulation/ONCOPROTEIN / gata-1 / ldb1 / lmo2 / fog-1 / Transcription regulation-ONCOPROTEIN complex | ||||||
Function / homology | Function and homology information lymph gland plasmatocyte differentiation / lymph gland crystal cell differentiation / negative regulation of hemocyte differentiation / amnioserosa maintenance / positive regulation of antibacterial peptide biosynthetic process / regulation of primitive erythrocyte differentiation / basophil differentiation / eosinophil fate commitment / regulation of definitive erythrocyte differentiation / germ-band shortening ...lymph gland plasmatocyte differentiation / lymph gland crystal cell differentiation / negative regulation of hemocyte differentiation / amnioserosa maintenance / positive regulation of antibacterial peptide biosynthetic process / regulation of primitive erythrocyte differentiation / basophil differentiation / eosinophil fate commitment / regulation of definitive erythrocyte differentiation / germ-band shortening / regulation of kinase activity / cellular component assembly / Factors involved in megakaryocyte development and platelet production / larval lymph gland hemopoiesis / negative regulation of erythrocyte differentiation / lymph gland development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / megakaryocyte differentiation / compound eye development / regulation of glycoprotein biosynthetic process / chaeta development / positive regulation of hemoglobin biosynthetic process / cerebellar Purkinje cell differentiation / head development / epithelial structure maintenance / myeloid cell apoptotic process / primitive erythrocyte differentiation / osteoblast proliferation / cell development / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / bHLH transcription factor binding / beta-catenin-TCF complex / Sertoli cell development / RUNX1 regulates transcription of genes involved in differentiation of HSCs / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / LIM domain binding / negative regulation of bone mineralization / dendritic cell differentiation / cellular response to follicle-stimulating hormone stimulus / Factors involved in megakaryocyte development and platelet production / positive regulation of mast cell degranulation / negative regulation of myeloid cell apoptotic process / myeloid cell differentiation / C2H2 zinc finger domain binding / gastrulation with mouth forming second / cellular response to thyroid hormone stimulus / anterior/posterior axis specification / embryonic hemopoiesis / platelet formation / erythrocyte development / regulation of focal adhesion assembly / DNA-binding transcription repressor activity / bone mineralization / positive regulation of osteoblast proliferation / cell leading edge / somatic stem cell population maintenance / positive regulation of cell adhesion / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / hair follicle development / cell fate commitment / animal organ regeneration / cis-regulatory region sequence-specific DNA binding / homeostasis of number of cells within a tissue / regulation of cell migration / cellular response to cAMP / negative regulation of insulin receptor signaling pathway / transcription repressor complex / cerebellum development / erythrocyte differentiation / positive regulation of erythrocyte differentiation / transcription coregulator binding / protein-DNA complex / positive regulation of transcription elongation by RNA polymerase II / RNA polymerase II transcription regulatory region sequence-specific DNA binding / transcription coactivator binding / chromatin DNA binding / neuron differentiation / platelet aggregation / Wnt signaling pathway / RNA polymerase II transcription regulator complex / male gonad development / : / positive regulation of peptidyl-tyrosine phosphorylation / sequence-specific double-stranded DNA binding / p53 binding / cell-cell signaling / nervous system development / heart development / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / in utero embryonic development / cellular response to lipopolysaccharide / cell population proliferation / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / cell differentiation / transcription coactivator activity Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Drosophila melanogaster (fruit fly) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Wilkinson-White, L. / Gamsjaeger, R. / Dastmalchi, S. / Wienert, B. / Stokes, P.H. / Crossley, M. / Mackay, J.P. / Matthews, J.M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Structural basis of simultaneous recruitment of the transcriptional regulators LMO2 and FOG1/ZFPM1 by the transcription factor GATA1 Authors: Wilkinson-White, L. / Gamsjaeger, R. / Dastmalchi, S. / Wienert, B. / Stokes, P.H. / Crossley, M. / Mackay, J.P. / Matthews, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2l6z.cif.gz | 556.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2l6z.ent.gz | 484.1 KB | Display | PDB format |
PDBx/mmJSON format | 2l6z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l6/2l6z ftp://data.pdbj.org/pub/pdb/validation_reports/l6/2l6z | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 4417.993 Da / Num. of mol.: 1 / Fragment: GATA-type 1 domain, residues 200-238 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P17679 |
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#2: Protein/peptide | Mass: 3961.636 Da / Num. of mol.: 1 / Fragment: UNP residues 202-235 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9VPQ6 |
#3: Protein | Mass: 10564.112 Da / Num. of mol.: 1 Fragment: residues 84-155; LIM-binding domain (LID), UNP residues 336-348 Mutation: C130S Source method: isolated from a genetically manipulated source Details: including a flexible linker region, GGSGGSGGSGG / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) References: UniProt: Q544Z2, UniProt: P70662, UniProt: P25801*PLUS |
#4: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 2D 1H-15N HSQC |
-Sample preparation
Details | Contents: 1mM [U-100% 15N] GATA1NF; 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 1 mM / Component: entity_1-1 / Isotopic labeling: [U-100% 15N] |
Sample conditions | Ionic strength: 0.12 / pH: 6.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 800 MHz |
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-Processing
NMR software | Name: CNS / Developer: Brunger, Adams, Clore, Gros, Nilges and Read / Classification: refinement |
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Refinement | Method: simulated annealing / Software ordinal: 1 / Details: haddock 2.1 based on cns |
NMR representative | Selection criteria: lowest energy |
NMR ensemble | Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 10 / Conformers submitted total number: 10 / Representative conformer: 1 |