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- PDB-2l6y: haddock model of GATA1NF:Lmo2LIM2-Ldb1LID -

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Basic information

Entry
Database: PDB / ID: 2l6y
Titlehaddock model of GATA1NF:Lmo2LIM2-Ldb1LID
Components
  • Erythroid transcription factor
  • LIM domain only 2, linker, LIM domain-binding protein 1
KeywordsTranscription 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 / positive regulation of hemoglobin biosynthetic process / cerebellar Purkinje cell differentiation ...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 / positive regulation of hemoglobin biosynthetic process / cerebellar Purkinje cell differentiation / primitive erythrocyte differentiation / myeloid cell apoptotic process / megakaryocyte differentiation / head development / osteoblast proliferation / cell development / beta-catenin-TCF complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RUNX1 regulates transcription of genes involved in differentiation of HSCs / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / epithelial structure maintenance / LIM domain binding / Sertoli cell development / dendritic cell differentiation / negative regulation of bone mineralization / Factors involved in megakaryocyte development and platelet production / cellular response to follicle-stimulating hormone stimulus / 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 / DNA binding, bending / platelet formation / regulation of focal adhesion assembly / positive regulation of osteoblast proliferation / erythrocyte development / bone mineralization / cell leading edge / somatic stem cell population maintenance / animal organ regeneration / hair follicle development / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / cis-regulatory region sequence-specific DNA binding / transcription repressor complex / homeostasis of number of cells within a tissue / positive regulation of cell adhesion / regulation of cell migration / positive regulation of erythrocyte differentiation / cellular response to cAMP / cerebellum development / erythrocyte differentiation / transcription coregulator binding / positive regulation of transcription elongation by RNA polymerase II / protein-DNA complex / chromatin DNA binding / platelet aggregation / transcription coactivator binding / RNA polymerase II transcription regulator complex / Wnt signaling pathway / neuron differentiation / p53 binding / cell-cell signaling / cellular response to lipopolysaccharide / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / DNA-binding transcription factor binding / in utero embryonic development / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / cell population proliferation / cell adhesion / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / chromatin binding / chromatin / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / identical protein binding / nucleus
Similarity search - Function
: / LIM-domain binding protein/SEUSS / LIM interaction domain / LIM-domain binding protein / LIM interaction domain (LID) / LIM interaction domain (LID) domain profile. / Transcription factor GATA / GATA-type zinc finger domain. / GATA-type zinc finger domain profile. / zinc finger binding to DNA consensus sequence [AT]GATA[AG] ...: / LIM-domain binding protein/SEUSS / LIM interaction domain / LIM-domain binding protein / LIM interaction domain (LID) / LIM interaction domain (LID) domain profile. / 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 / Cysteine Rich Protein / Cysteine Rich Protein / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / Ribbon / Zinc finger, NHR/GATA-type / Mainly Beta
Similarity search - Domain/homology
Erythroid transcription factor / Rhombotin-2 / LIM domain-binding protein 1 / Rhombotin-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsWilkinson-White, L. / Gamsjaeger, R. / Dastmalchi, S. / Wienert, B. / Stokes, P.H. / Crossley, M. / Mackay, J.P. / Matthews, J.M.
CitationJournal: 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
DepositionDec 1, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Database references / Structure summary
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_ref_seq / 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 / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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: Erythroid transcription factor
B: LIM domain only 2, linker, LIM domain-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1785
Polymers14,9822
Non-polymers1963
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Erythroid transcription factor / Eryf1 / GATA-binding factor 1 / GATA-1 / GF-1 / NF-E1 DNA-binding protein


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
#2: Protein LIM domain only 2, linker, LIM domain-binding protein 1 / LMO2 / LDB1 / Carboxyl-terminal LIM domain-binding protein 2 / CLIM-2 / LIM domain-binding factor ...LMO2 / LDB1 / Carboxyl-terminal LIM domain-binding protein 2 / CLIM-2 / LIM domain-binding factor CLIM2 / mLdb1 / Nuclear LIM interactor


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 ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-15N HSQC

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Sample preparation

DetailsContents: 1mM [U-15N] GATA1NF; 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: entity_1-1 / Isotopic labeling: [U-15N]
Sample conditionsIonic strength: 0.12 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR softwareName: CNS / Developer: Brunger, Adams, Clore, Gros, Nilges and Read / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: haddock (2.1) model
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 10 / Representative conformer: 1

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