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- PDB-3g8x: GR DNA binding domain:GilZ 16bp complex-65 -

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Basic information

Entry
Database: PDB / ID: 3g8x
TitleGR DNA binding domain:GilZ 16bp complex-65
Components
  • DNA (5'-D(*AP*AP*GP*AP*AP*CP*AP*TP*TP*GP*GP*GP*TP*TP*CP*C)-3')
  • DNA (5'-D(*TP*GP*GP*AP*AP*CP*CP*CP*AP*AP*TP*GP*TP*TP*CP*T)-3')
  • Glucocorticoid receptor
KeywordsTRANSCRIPTION/DNA / glucocorticoid / DNA-binding / allostery / lever arm / transcription / hormone / Alternative initiation / Chromatin regulator / Cytoplasm / Lipid-binding / Metal-binding / Nucleus / Phosphoprotein / Polymorphism / Receptor / Steroid-binding / Transcription regulation / Ubl conjugation / Zinc / Zinc-finger / TRANSCRIPTION-DNA COMPLEX
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 / spindle / receptor tyrosine kinase binding / 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
DNA / DNA (> 10) / Glucocorticoid receptor
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsPufall, M.A. / Yamamoto, K.R. / Meijsing, S.H.
CitationJournal: Science / Year: 2009
Title: DNA binding site sequence directs glucocorticoid receptor structure and activity.
Authors: Meijsing, S.H. / Pufall, M.A. / So, A.Y. / Bates, D.L. / Chen, L. / Yamamoto, K.R.
History
DepositionFeb 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 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 / 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 / _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
A: Glucocorticoid receptor
B: Glucocorticoid receptor
D: DNA (5'-D(*TP*GP*GP*AP*AP*CP*CP*CP*AP*AP*TP*GP*TP*TP*CP*T)-3')
C: DNA (5'-D(*AP*AP*GP*AP*AP*CP*AP*TP*TP*GP*GP*GP*TP*TP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,10710
Polymers29,7214
Non-polymers3866
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-35 kcal/mol
Surface area12840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.213, 37.914, 96.993
Angle α, β, γ (deg.)90.00, 123.22, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glucocorticoid receptor / / GR / Nuclear receptor subfamily 3 group C member 1


Mass: 9962.758 Da / Num. of mol.: 2 / Fragment: UNP residues 440-525
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grl, Nr3c1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: P06536

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DNA chain , 2 types, 2 molecules DC

#2: DNA chain DNA (5'-D(*TP*GP*GP*AP*AP*CP*CP*CP*AP*AP*TP*GP*TP*TP*CP*T)-3')


Mass: 4873.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: oligonucleotide from Integrated DNA technologies
#3: DNA chain DNA (5'-D(*AP*AP*GP*AP*AP*CP*AP*TP*TP*GP*GP*GP*TP*TP*CP*C)-3')


Mass: 4922.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: oligonucleotide from Integrated DNA technologies

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Non-polymers , 3 types, 73 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50mM Na Cacodylate, pH 7.0, 2.25mM Spermine, 9mM MgCl2, 1.8 CoCl2, 5% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1CacodylateCacodylic acid11
2MgCl211
3CacodylateCacodylic acid12
4MgCl212
5CoCl212
6Spermine12
7PEG 800012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 26, 2007
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 2.05→40 Å / Num. obs: 21522 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 41.139 Å2 / Rmerge(I) obs: 0.137 / Rsym value: 0.183 / Net I/σ(I): 15
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1604 / Rsym value: 0.659 / % possible all: 71.1

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GLU

1glu


Resolution: 2.05→35.363 Å / SU ML: 2.04 / σ(F): 0.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2574 1836 9.38 %
Rwork0.2095 --
obs0.2138 19577 84.72 %
all-21522 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.89 Å2 / ksol: 0.311 e/Å3
Displacement parametersBiso mean: 84.4 Å2
Refinement stepCycle: LAST / Resolution: 2.05→35.363 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1160 650 12 67 1889
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_d1.323
X-RAY DIFFRACTIONf_bond_d0.01
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.05-2.11380.39121070.343297197147
2.1138-2.19850.33171460.27541482148270
2.1985-2.29850.22931570.23491570157077
2.2985-2.41970.26861860.24561736173684
2.4197-2.57120.26391830.24581838183888
2.5712-2.76970.31162130.21881877187791
2.7697-3.04830.24711970.23811946194692
3.0483-3.4890.2892110.22532033203397
3.489-4.39450.22372190.18532107210799
4.3945-35.3680.24072170.184921812181100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.25160.63581.82380.55350.62832.04810.25670.2381-1.1676-0.0907-0.0571-0.3529-0.02460.3316-0.22820.2688-0.01110.01370.27160.03960.5415-19.6368-14.04790.599
22.80280.98840.4731-0.00971.50450.3849-0.40710.887-0.1443-0.6461-0.07710.4363-0.89550.0660.37760.71980.0094-0.12110.5431-0.05930.3459-35.5103-19.573-21.6838
33.49371.5352.64672.69112.90683.4085-0.43810.2641-0.4397-0.65220.9439-0.2349-0.96570.21-0.5630.5557-0.3093-0.01021.05240.08580.3703-14.3378-13.1651-18.1041
4-1.36253.85754.02013.54852.48523.9627-0.55641.015-0.6794-0.40730.6407-0.5346-0.94430.7893-0.18980.4256-0.02480.03561.4365-0.22190.517-16.2331-16.0535-21.805
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain A
2X-RAY DIFFRACTION2Chain B
3X-RAY DIFFRACTION3Chain C
4X-RAY DIFFRACTION4Chain D

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