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- PDB-3g9p: GR DNA binding domain:Sgk 16bp complex-7 -

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Basic information

Entry
Database: PDB / ID: 3g9p
TitleGR DNA binding domain:Sgk 16bp complex-7
Components
  • DNA (5'-D(*AP*AP*GP*AP*AP*CP*AP*TP*TP*TP*TP*GP*TP*CP*CP*G)-3')
  • DNA (5'-D(*TP*CP*GP*GP*AP*CP*AP*AP*AP*AP*TP*GP*TP*TP*CP*T)-3')
  • Glucocorticoid receptor
KeywordsTRANSCRIPTION/DNA / glucocorticoid / DNA-binding / allostry / lever arm / hormone / Alternative initiation / Chromatin regulator / Cytoplasm / Lipid-binding / Metal-binding / Nucleus / Phosphoprotein / Polymorphism / Receptor / Steroid-binding / Transcription / 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 / intracellular 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 / intracellular 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 / motor behavior / positive regulation of dendritic spine development / 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
DNA / DNA (> 10) / Glucocorticoid receptor
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.652 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 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 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
B: Glucocorticoid receptor
A: Glucocorticoid receptor
C: DNA (5'-D(*TP*CP*GP*GP*AP*CP*AP*AP*AP*AP*TP*GP*TP*TP*CP*T)-3')
D: DNA (5'-D(*AP*AP*GP*AP*AP*CP*AP*TP*TP*TP*TP*GP*TP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9828
Polymers29,7204
Non-polymers2624
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-21 kcal/mol
Surface area12370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.382, 38.470, 97.039
Angle α, β, γ (deg.)90.00, 123.44, 90.00
Int Tables number5
Space group name H-MC121

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Components

#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: Nr3c1, Grl / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: P06536
#2: DNA chain DNA (5'-D(*TP*CP*GP*GP*AP*CP*AP*AP*AP*AP*TP*GP*TP*TP*CP*T)-3')


Mass: 4897.203 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Glucocorticoid receptor binding site: Sgk 16 base top strand
#3: DNA chain DNA (5'-D(*AP*AP*GP*AP*AP*CP*AP*TP*TP*TP*TP*GP*TP*CP*CP*G)-3')


Mass: 4897.203 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Glucocorticoid receptor binding site: Sgk 16 base bottom strand
#4: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 177 / 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: 3.08 Å3/Da / Density % sol: 60.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50mM MES, pH 6.0, 20mM MgCl2, 15% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1MES11
2MgCl211
3MES12
4MgCl212
5isopropanol12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115878 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 12, 2007
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115878 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 42923 / % possible obs: 88.2 % / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 23.068 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.078 / Net I/σ(I): 19.5
Reflection shellResolution: 1.59→1.65 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 1.7 / Num. unique all: 1664 / Rsym value: 0.53 / % possible all: 34.6

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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: 1GLU

1glu


Resolution: 1.652→34.354 Å / SU ML: 1.4 / σ(F): 0.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2029 1816 5.03 %PHENIX - Automatic
Rwork0.1767 ---
obs0.178 36121 82.38 %-
all-42923 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.535 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 50.2 Å2
Refinement stepCycle: LAST / Resolution: 1.652→34.354 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1159 650 4 177 1990
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_d1.487
X-RAY DIFFRACTIONf_bond_d0.011
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.652-1.7110.2919770.27241519126037
1.711-1.77950.24251270.24182319217856
1.7795-1.86050.25291510.23412898332270
1.8605-1.95860.23331660.20873300374480
1.9586-2.08130.1952150.19713738415091
2.0813-2.24190.18782070.17743971450996
2.2419-2.46750.19672180.17074038451297
2.4675-2.82440.19962110.17774113451699
2.8244-3.55790.21652210.18864135466098
3.5579-34.36120.18992230.15624274477399
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)
12.21450.36150.83471.7627-0.56431.77290.195-0.0826-0.27070.0121-0.09690.0770.0381-0.2163-0.06360.28080.00380.020.2532-0.02490.344519.964318.5378-0.332
22.2192-0.45090.22931.44380.80111.0136-0.308-0.69130.07930.44940.1478-0.31020.16480.26250.09250.42880.0488-0.07530.4385-0.00450.325435.545414.360121.3725
32.2847-0.7371-0.09922.0988-1.07571.6184-0.3309-0.6858-0.60920.43720.71590.0893-0.5895-0.7908-0.25420.44750.14610.02550.60320.03860.229714.589320.141817.9455
4-0.4157-1.46520.39672.0295-1.65462.0512-0.4594-0.6083-0.4250.42910.55740.3225-0.8257-0.6342-0.11250.43630.09160.07060.72030.11110.298816.395617.183721.7643
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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