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- PDB-1rgd: STRUCTURE REFINEMENT OF THE GLUCOCORTICOID RECEPTOR-DNA BINDING D... -

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Entry
Database: PDB / ID: 1rgd
TitleSTRUCTURE REFINEMENT OF THE GLUCOCORTICOID RECEPTOR-DNA BINDING DOMAIN FROM NMR DATA BY RELAXATION MATRIX CALCULATIONS
ComponentsGLUCOCORTICOID RECEPTOR
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN
Function / homology
Function and homology information


muscle atrophy / negative regulation of synaptic plasticity / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of glucocorticoid receptor signaling pathway / response to inactivity / glucocorticoid receptor signaling pathway / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / positive regulation of cell growth involved in cardiac muscle cell development / SUMOylation of intracellular receptors ...muscle atrophy / negative regulation of synaptic plasticity / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of glucocorticoid receptor signaling pathway / response to inactivity / glucocorticoid receptor signaling pathway / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / positive regulation of cell growth involved in cardiac muscle cell development / SUMOylation of intracellular receptors / response to mercury ion / hormone binding / Nuclear Receptor transcription pathway / steroid hormone binding / glucocorticoid metabolic process / neuroinflammatory response / microglia differentiation / maternal behavior / mammary gland duct morphogenesis / nucleus localization / cellular response to magnesium ion / response to arsenic-containing substance / astrocyte differentiation / negative regulation of vascular permeability / positive regulation of glutamate secretion / cellular response to glucocorticoid stimulus / positive regulation of dendritic spine development / motor behavior / regulation of gluconeogenesis / adrenal gland development / cellular response to steroid hormone stimulus / response to corticosterone / response to dexamethasone / postsynaptic density, intracellular component / androgen metabolic process / regulation of glucose metabolic process / estrogen response element binding / response to electrical stimulus / intracellular steroid hormone receptor signaling pathway / core promoter sequence-specific DNA binding / transcription initiation-coupled chromatin remodeling / Hsp70 protein binding / cellular response to transforming growth factor beta stimulus / heat shock protein binding / TBP-class protein binding / steroid binding / cellular response to dexamethasone stimulus / response to activity / synaptic transmission, glutamatergic / female pregnancy / RNA polymerase II transcription regulatory region sequence-specific DNA binding / lung development / Hsp90 protein binding / response to insulin / receptor tyrosine kinase binding / spindle / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / response to calcium ion / circadian rhythm / positive regulation of neuron apoptotic process / nuclear receptor activity / sequence-specific double-stranded DNA binding / gene expression / regulation of cell population proliferation / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / protein-containing complex assembly / sequence-specific DNA binding / dendritic spine / transcription coactivator activity / nuclear speck / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / centrosome / negative regulation of DNA-templated transcription / glutamatergic synapse / chromatin binding / protein-containing complex binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / zinc ion binding / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Glucocorticoid receptor / Glucocorticoid receptor / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors ...Glucocorticoid receptor / Glucocorticoid receptor / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Glucocorticoid receptor
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR
AuthorsVan Tilborg, M.A.A. / Bonvin, A.M.J.J. / Hard, K. / Davis, A. / Maler, B. / Boelens, R. / Yamamoto, K.R. / Kaptein, R.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Structure refinement of the glucocorticoid receptor-DNA binding domain from NMR data by relaxation matrix calculations.
Authors: van Tilborg, M.A. / Bonvin, A.M. / Hard, K. / Davis, A.L. / Maler, B. / Boelens, R. / Yamamoto, K.R. / Kaptein, R.
#1: Journal: Nature / Year: 1991
Title: Crystallographic Analysis of the Interaction of the Glucocorticoid Receptor with DNA
Authors: Luisi, B.F. / Xu, W.X. / Otwinowski, Z. / Freedman, L.P. / Yamamoto, K.R. / Sigler, P.B.
#2: Journal: Science / Year: 1990
Title: Solution Structure of the Glucocorticoid Receptor DNA-Binding Domain
Authors: Hard, T. / Kellenbach, E. / Boelens, R. / Maler, B.A. / Dahlman, K. / Freedman, L.P. / Carlstedt-Duke, J. / Yamamoto, K.R. / Gustafsson, J.-A. / Kaptein, R.
#3: Journal: Biochemistry / Year: 1990
Title: 1H NMR Studies of the Glucocorticoid Receptor DNA-Binding Domain: Sequential Assignments and Identification of Secondary Structure Elements
Authors: Hard, T. / Kellenbach, E. / Boelens, R. / Kaptein, R. / Dahlman, K. / Carlstedt-Duke, J. / Freedman, L.P. / Maler, B.A. / Hyde, E. / Gustafsson, J.-A. / Yamamoto, K.R.
History
DepositionJan 6, 1995Processing site: BNL
Revision 1.0Feb 14, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_keywords / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_keywords.text / _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: GLUCOCORTICOID RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0933
Polymers7,9621
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / -
Representative

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Components

#1: Protein GLUCOCORTICOID RECEPTOR /


Mass: 7962.345 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / References: UniProt: P06536
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

NMR software
NameClassification
IRMArefinement
DINOSAURrefinement
NMR ensembleConformers submitted total number: 11

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