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- PDB-3g9m: GR DNA-binding domain:Sgk 16bp complex-44 -

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Basic information

Entry
Database: PDB / ID: 3g9m
TitleGR DNA-binding domain:Sgk 16bp complex-44
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 / 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


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 / negative regulation of long-term synaptic depression / response to inactivity / 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 / negative regulation of long-term synaptic depression / response to inactivity / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / SUMOylation of intracellular receptors / positive regulation of cell growth involved in cardiac muscle cell development / Nuclear Receptor transcription pathway / response to mercury ion / steroid hormone binding / 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 / regulation of gluconeogenesis / cellular response to glucocorticoid stimulus / 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 / associative learning / regulation of glucose metabolic process / 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 / heat shock protein binding / steroid 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 / protein-containing complex assembly / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / dendritic spine / gene expression / 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
DNA / DNA (> 10) / Glucocorticoid receptor
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 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 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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*CP*GP*GP*AP*CP*AP*AP*AP*AP*TP*GP*TP*TP*CP*T)-3')
C: 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)30,10610
Polymers29,7204
Non-polymers3866
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-28 kcal/mol
Surface area13020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.058, 38.713, 96.475
Angle α, β, γ (deg.)90.00, 123.71, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-101-

HOH

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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: Nr3c1, Grl / 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*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: GR binding site: Sgk 16 base bottom 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: GR binding site: Sgk 16 base top strand

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Non-polymers , 3 types, 260 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


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


Mass: 18.015 Da / Num. of mol.: 254 / 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: 3.09 Å3/Da / Density % sol: 60.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50mM Tris, pH 7.5, 200mM KCl, 50mM MgCl2, 10% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1Tris11
2KCl11
3MgCl211
4Tris12
5KCl12
6MgCl212
7PEG400012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 15, 2006
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.61→50 Å / Num. obs: 42461 / % possible obs: 90.4 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 21.16 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.044 / Net I/σ(I): 18.7
Reflection shellResolution: 1.61→1.67 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 1.6 / Num. unique all: 2595 / Rsym value: 0.374 / % possible all: 55.8

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Processing

Software
NameVersionClassification
HKL-2000data 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: 1.61→30.613 Å / SU ML: 1.56 / σ(F): 0.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1992 1760 4.65 %
Rwork0.1869 --
obs0.1875 37875 80.49 %
all-42461 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.345 Å2 / ksol: 0.396 e/Å3
Displacement parametersBiso mean: 44.8 Å2
Refinement stepCycle: LAST / Resolution: 1.61→30.613 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1244 650 12 254 2160
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_d1.328
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 (%)
1.61-1.67230.3015930.26571925192543
1.6723-1.73920.25091360.23182722272261
1.7392-1.81840.19661550.21583257325773
1.8184-1.91420.26421620.24823288328874
1.9142-2.03410.25461840.24163843384386
2.0341-2.19120.21172010.19174130413093
2.1912-2.41160.2491950.20023977397789
2.4116-2.76030.19242130.16734426442698
2.7603-3.4770.21732170.1754437443798
3.477-30.61890.15292040.16554110411089
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)
12.18790.14410.50420.96180.21750.60250.11480.0774-0.3338-0.0306-0.0563-0.1163-0.00140.1439-0.06420.1240.00280.00720.15920.01550.183712.534821.379840.9794
20.82050.1342-0.72180.4682-0.68511.0459-0.0440.317-0.0354-0.3110.06990.1350.087-0.3092-0.06440.272-0.0187-0.03760.2713-0.00580.1472-3.79215.635917.8667
32.35040.73171.27841.70641.16151.9556-0.15540.7416-0.323-0.37910.483-0.1081-0.56920.9721-0.25830.2127-0.12820.05150.425-0.06690.073817.776622.28522.1713
4-0.78971.53172.15441.44110.73613.5982-0.24360.7597-0.3056-0.29080.474-0.2699-0.52120.9703-0.21140.1895-0.03410.03720.6432-0.15220.162915.829519.351118.5334
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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