+Open data
-Basic information
Entry | Database: PDB / ID: 2l6y | ||||||
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Title | haddock model of GATA1NF:Lmo2LIM2-Ldb1LID | ||||||
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 regulation of primitive erythrocyte differentiation / basophil differentiation / eosinophil fate commitment / regulation of definitive erythrocyte differentiation / regulation of kinase activity / cellular component assembly / negative regulation of erythrocyte differentiation / regulation of glycoprotein biosynthetic process / megakaryocyte differentiation / positive regulation of hemoglobin biosynthetic process ...regulation of primitive erythrocyte differentiation / basophil differentiation / eosinophil fate commitment / regulation of definitive erythrocyte differentiation / regulation of kinase activity / cellular component assembly / negative regulation of erythrocyte differentiation / regulation of glycoprotein biosynthetic process / megakaryocyte differentiation / positive regulation of hemoglobin biosynthetic process / cerebellar Purkinje cell differentiation / epithelial structure maintenance / myeloid cell apoptotic process / head development / 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 / dendritic cell differentiation / cellular response to follicle-stimulating hormone stimulus / negative regulation of bone mineralization / 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 / anterior/posterior axis specification / embryonic hemopoiesis / platelet formation / erythrocyte development / regulation of focal adhesion assembly / bone mineralization / positive regulation of osteoblast proliferation / cell leading edge / somatic stem cell population maintenance / positive regulation of cell adhesion / hair follicle development / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / cell fate commitment / animal organ regeneration / cis-regulatory region sequence-specific DNA binding / homeostasis of number of cells within a tissue / cellular response to cAMP / regulation of cell migration / 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 / neuron differentiation / chromatin DNA binding / 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 / 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 / transcription coactivator activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell adhesion / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / chromatin binding / chromatin / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
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 | 2l6y.cif.gz | 445.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2l6y.ent.gz | 374.7 KB | Display | PDB format |
PDBx/mmJSON format | 2l6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l6/2l6y ftp://data.pdbj.org/pub/pdb/validation_reports/l6/2l6y | 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 | 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 |
#3: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 2D 1H-15N HSQC |
-Sample preparation
Details | Contents: 1mM [U-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-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) model |
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 |