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- PDB-1glu: CRYSTALLOGRAPHIC ANALYSIS OF THE INTERACTION OF THE GLUCOCORTICOI... -

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Basic information

Entry
Database: PDB / ID: 1glu
TitleCRYSTALLOGRAPHIC ANALYSIS OF THE INTERACTION OF THE GLUCOCORTICOID RECEPTOR WITH DNA
Components
  • DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*TP*CP*GP*AP*TP*GP*TP*TP*C P*TP*G)-3')
  • PROTEIN (GLUCOCORTICOID RECEPTOR)
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / 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 / Resolution: 2.9 Å
AuthorsLuisi, B.F. / Xu, W.X. / Otwinowski, Z. / Freedman, L.P. / Yamamoto, K.R. / Sigler, P.B.
CitationJournal: 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.
History
DepositionAug 30, 1992Deposition site: BNL / Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*TP*CP*GP*AP*TP*GP*TP*TP*C P*TP*G)-3')
D: DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*TP*CP*GP*AP*TP*GP*TP*TP*C P*TP*G)-3')
A: PROTEIN (GLUCOCORTICOID RECEPTOR)
B: PROTEIN (GLUCOCORTICOID RECEPTOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1398
Polymers29,8774
Non-polymers2624
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.500, 95.700, 120.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: LYS A 435 - PRO A 436 OMEGA ANGLE = 121.694 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATIO

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Components

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


Mass: 5804.773 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein PROTEIN (GLUCOCORTICOID RECEPTOR)


Mass: 9133.866 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: LIVER
Gene (production host): GENE FRAGMENT (AMINO ACIDS 440 TO 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.: 41 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST SIX AMINO ACID RESIDUES ARE CLONAL LINKERS, THEY ARE DIFFERENT FROM THE NATURAL SEQUENCE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.71 Å3/Da / Density % sol: 66.89 %
Crystal growTemperature: 281 K / Method: vapor diffusion / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION, temperature 281.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MG SULFATE11
3NACL11
4NA CACODYLATE11
5SPERMINE11
6ZNCL211
7WATER12
8MPD/ETOH12
9NACL12
10NA CACODYLATE12
Crystal grow
*PLUS
Temperature: 8 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.07 mMDNA1dropduplex
20.14 mM440-5251drop
31.8 mM1dropMgSO4
425 mM1dropNaCl
518 mMsodium cacodylate1drop
61.8 mMspermine1drop
70.002 mM1dropZnCl2
80.2 M1reservoirNaCl
924 mMsodium cacodylate1reservoir
108 %MPD1reservoircan be replaced with ethanol

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Data collection

DiffractionMean temperature: 263 K
Diffraction sourceSource: ROTATING ANODE
DetectorType: SDMS / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORrefinement
PROLSQrefinement
RefinementRfactor Rwork: 0.196 / Rfactor obs: 0.196 / Highest resolution: 2.9 Å
Refinement stepCycle: LAST / Highest resolution: 2.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1256 770 4 41 2071
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 6.5 Å / Num. reflection obs: 7669 / Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.4

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