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- PDB-1r4o: Crystallographic analysis of the interaction of the glucocorticoi... -

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Basic information

Entry
Database: PDB / ID: 1r4o
TitleCrystallographic analysis of the interaction of the glucocorticoid receptor with DNA
Components
  • 5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*TP*CP*GP*AP*TP*GP*TP*TP*CP*TP*G)-3'
  • Glucocorticoid receptor
KeywordsTRANSCRIPTION/DNA / GR / Steroid receptor / Protein-DNA Complex / Glucocorticoid / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


nuclear receptor-mediated corticosteroid signaling pathway / positive regulation of nuclear receptor-mediated glucocorticoid signaling pathway / muscle atrophy / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / negative regulation of synaptic plasticity / response to inactivity / negative regulation of long-term synaptic depression / nuclear receptor-mediated glucocorticoid signaling pathway / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity ...nuclear receptor-mediated corticosteroid signaling pathway / positive regulation of nuclear receptor-mediated glucocorticoid signaling pathway / muscle atrophy / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / negative regulation of synaptic plasticity / response to inactivity / negative regulation of long-term synaptic depression / nuclear receptor-mediated glucocorticoid signaling pathway / 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 / hormone binding / neuroinflammatory response / mammary gland duct morphogenesis / microglia differentiation / cellular response to magnesium ion / astrocyte differentiation / maternal behavior / response to arsenic-containing substance / negative regulation of vascular permeability / positive regulation of glutamate secretion / cellular response to glucocorticoid stimulus / motor behavior / response to corticosterone / positive regulation of dendritic spine development / regulation of gluconeogenesis / adrenal gland development / cellular response to steroid hormone stimulus / response to dexamethasone / androgen metabolic process / regulation of glucose metabolic process / estrogen response element binding / postsynaptic density, intracellular component / nuclear receptor-mediated steroid hormone signaling pathway / response to electrical stimulus / core promoter sequence-specific DNA binding / cellular response to transforming growth factor beta stimulus / steroid binding / heat shock protein binding / TBP-class protein binding / Hsp70 protein binding / cellular response to dexamethasone stimulus / transcription initiation-coupled chromatin remodeling / response to activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / synaptic transmission, glutamatergic / female pregnancy / response to insulin / lung development / Hsp90 protein binding / receptor tyrosine kinase binding / positive regulation of miRNA transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / spindle / response to calcium ion / nuclear receptor activity / circadian rhythm / sequence-specific double-stranded DNA binding / positive regulation of neuron apoptotic process / regulation of cell population proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / protein-containing complex assembly / double-stranded DNA binding / gene expression / dendritic spine / sequence-specific DNA binding / transcription coactivator activity / nuclear speck / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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-containing complex binding / negative regulation of apoptotic process / protein kinase binding / chromatin / 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 / nucleus / membrane / 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 / 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
DNA / DNA (> 10) / Glucocorticoid receptor
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLuisi, B.F. / Xu, W.X. / Otwinowski, Z. / Freedman, L.P. / Yamamoto, K.R. / Sigler, P.B.
Citation
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.
#1: Journal: Nat.Struct.Biol. / Year: 1995
Title: The basis for half-site specificity explored through a non-cognate steroid receptor-DNA complex
Authors: Gewirth, D.T. / Sigler, P.B.
History
DepositionOct 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 22, 2014Group: Refinement description
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_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_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

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*TP*CP*GP*AP*TP*GP*TP*TP*CP*TP*G)-3'
D: 5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*TP*CP*GP*AP*TP*GP*TP*TP*CP*TP*G)-3'
A: Glucocorticoid receptor
B: Glucocorticoid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3368
Polymers32,0744
Non-polymers2624
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.5, 97.5, 120.5
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain 5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*TP*CP*GP*AP*TP*GP*TP*TP*CP*TP*G)-3'


Mass: 5804.773 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Glucocorticoid response element with 4 bp of spacer between half-sites
#2: Protein Glucocorticoid receptor / GR


Mass: 10232.162 Da / Num. of mol.: 2 / Fragment: DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: NR3C1 OR GRL / Plasmid: pT7440-525 / Production host: Escherichia coli (E. coli) / References: UniProt: P06536
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.48 Å3/Da / Density % sol: 64.62 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MPD, sodium cacodylate, sodium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2sodium cacodylate11
3sodium chloride11
4H2O11
5MPD12
6sodium cacodylate12
7H2O12

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Data collection

DiffractionMean temperature: 263 K
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→19.67 Å / Num. obs: 14846

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GLU

1glu


Resolution: 2.5→6 Å / Rfactor obs: 0.196
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1238 770 4 109 2121

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