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- PDB-1gdc: REFINED SOLUTION STRUCTURE OF THE GLUCOCORTICOID RECEPTOR DNA-BIN... -

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Entry
Database: PDB / ID: 1gdc
TitleREFINED SOLUTION STRUCTURE OF THE GLUCOCORTICOID RECEPTOR DNA-BINDING DOMAIN
ComponentsGLUCOCORTICOID RECEPTOR
KeywordsGLUCOCORTICOID RECEPTOR
Function / homology
Function and homology information


nuclear receptor-mediated corticosteroid signaling pathway / negative regulation of behavioral fear response / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / muscle atrophy / negative regulation of synaptic plasticity / positive regulation of nuclear receptor-mediated glucocorticoid signaling pathway / nuclear receptor-mediated glucocorticoid signaling pathway / response to inactivity / negative regulation of long-term synaptic depression / regulation of glucocorticoid biosynthetic process ...nuclear receptor-mediated corticosteroid signaling pathway / negative regulation of behavioral fear response / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / muscle atrophy / negative regulation of synaptic plasticity / positive regulation of nuclear receptor-mediated glucocorticoid signaling pathway / nuclear receptor-mediated glucocorticoid signaling pathway / response to inactivity / negative regulation of long-term synaptic depression / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / SUMOylation of intracellular receptors / positive regulation of cell growth involved in cardiac muscle cell development / steroid hormone binding / Nuclear Receptor transcription pathway / response to mercury ion / glucocorticoid metabolic process / response to cortisol / neuroinflammatory response / Leydig cell differentiation / mammary gland duct morphogenesis / microglia differentiation / cellular response to magnesium ion / maternal behavior / response to arsenic-containing substance / astrocyte differentiation / negative regulation of vascular permeability / positive regulation of glutamate secretion / adrenal gland development / cellular response to glucocorticoid stimulus / regulation of gluconeogenesis / response to corticosterone / cellular response to steroid hormone stimulus / response to dexamethasone / positive regulation of dendritic spine development / motor behavior / hormone binding / androgen metabolic process / regulation of glucose metabolic process / associative learning / response to electrical stimulus / estrogen response element binding / cellular response to dexamethasone stimulus / nuclear receptor-mediated steroid hormone signaling pathway / cellular response to transforming growth factor beta stimulus / postsynaptic density, intracellular component / core promoter sequence-specific DNA binding / steroid binding / heat shock protein binding / Hsp70 protein binding / transcription initiation-coupled chromatin remodeling / lung development / TBP-class protein binding / positive regulation of cytokine production / response to activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / synaptic transmission, glutamatergic / promoter-specific chromatin binding / Hsp90 protein binding / female pregnancy / response to insulin / circadian rhythm / response to calcium ion / receptor tyrosine kinase binding / response to wounding / positive regulation of miRNA transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / spindle / nuclear receptor activity / sequence-specific double-stranded DNA binding / positive regulation of neuron apoptotic process / regulation of cell population proliferation / double-stranded DNA binding / protein-containing complex assembly / DNA-binding transcription activator activity, RNA polymerase II-specific / gene expression / dendritic spine / sequence-specific DNA binding / transcription coactivator activity / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / centrosome / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / negative regulation of apoptotic process / chromatin / protein-containing complex binding / glutamatergic synapse / 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 / identical protein binding
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 / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. ...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 / Double treble clef zinc finger, C4 type / 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
AuthorsBaumann, H. / Paulsen, K. / Kovacs, H. / Berglund, H. / Wright, A.P.H. / Gustafsson, J.-A. / Hard, T.
Citation
Journal: Biochemistry / Year: 1993
Title: Refined solution structure of the glucocorticoid receptor DNA-binding domain.
Authors: Baumann, H. / Paulsen, K. / Kovacs, H. / Berglund, H. / Wright, A.P. / Gustafsson, J.A. / Hard, T.
#1: Journal: Acc.Chem.Res. / Year: 1993
Title: Structure and Function of the DNA-Binding Domain of the Glucocorticoid Receptor and Other Members of the Nuclear Receptor Supergene Family
Authors: Hard, T. / Gustafsson, J.-A.
#2: Journal: Biochemistry / Year: 1992
Title: Backbone Dynamics of the Glucocorticoid Receptor DNA-Binding Domain
Authors: Berglund, H. / Kovacs, H. / Dahlman-Wright, K. / Gustafsson, J.-A. / Hard, T.
#3: 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.
#4: 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.
#5: 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.
History
DepositionMar 15, 1994Processing site: BNL
Revision 1.0Jun 22, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations / Other
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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: GLUCOCORTICOID RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2063
Polymers8,0761
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

#1: Protein GLUCOCORTICOID RECEPTOR


Mass: 8075.503 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
NameDeveloperClassification
DGIIHAVELrefinement
CHARMMBROOKSrefinement
NMR ensembleConformers submitted total number: 1

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