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- PDB-3g9j: GR DNA binding domain:Pal, 18bp complex-36 -

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Basic information

Entry
Database: PDB / ID: 3g9j
TitleGR DNA binding domain:Pal, 18bp complex-36
Components
  • DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*AP*AP*AP*TP*GP*TP*TP*CP*TP*G)-3')
  • DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*TP*TP*TP*TP*GP*TP*TP*CP*TP*G)-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 / positive regulation of cell growth involved in cardiac muscle cell development / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / steroid hormone binding / response to mercury ion / glucocorticoid metabolic process / response to cortisol / neuroinflammatory response / Leydig cell differentiation / mammary gland duct morphogenesis / microglia differentiation / response to arsenic-containing substance / maternal behavior / cellular response to magnesium ion / 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 / regulation of glucose metabolic process / associative learning / 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 / steroid binding / heat shock protein 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 calcium ion / circadian rhythm / response to insulin / receptor tyrosine kinase binding / positive regulation of miRNA transcription / response to wounding / 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 / DNA-binding transcription activator activity, RNA polymerase II-specific / double-stranded DNA binding / gene expression / sequence-specific DNA binding / dendritic spine / 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 / chromatin binding / centrosome / 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: 2.32 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 1.2Nov 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
C: DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*AP*AP*AP*TP*GP*TP*TP*CP*TP*G)-3')
D: DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*TP*TP*TP*TP*GP*TP*TP*CP*TP*G)-3')
A: Glucocorticoid receptor
B: Glucocorticoid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,42612
Polymers30,9164
Non-polymers5108
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-13 kcal/mol
Surface area12920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.069, 102.096, 112.076
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 2 types, 2 molecules CD

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


Mass: 5508.606 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: GR binding site: Pal 18bp top strand
#2: DNA chain DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*TP*TP*TP*TP*GP*TP*TP*CP*TP*G)-3')


Mass: 5481.564 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: GR binding site: Pal 18bp bottom strand

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Protein , 1 types, 2 molecules AB

#3: 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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Non-polymers , 3 types, 136 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 128 / 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: 3.62 Å3/Da / Density % sol: 65.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50mM HEPES, pH 7.0, 100mM KCl, 10mM CaCl2, 10% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1HEPES11
2KCl11
3CaCl211
4HEPES12
5KCl12
6CaCl212
7PEG40012

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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 Q315r / Detector: CCD / Date: Apr 25, 2008
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: 2.32→50 Å / Num. obs: 20142 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Biso Wilson estimate: 43.971 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.055 / Net I/σ(I): 23.1
Reflection shellResolution: 2.32→2.4 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 3.9 / Num. unique all: 1959 / Rsym value: 0.468 / % possible all: 100

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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: 2.32→49.125 Å / SU ML: 1.95 / σ(F): 0.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2255 1896 9.94 %PHENIX - Automatic
Rwork0.1844 ---
obs0.1884 19067 94.79 %-
all-20142 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.516 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso mean: 58.1 Å2
Refinement stepCycle: LAST / Resolution: 2.32→49.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1175 729 20 128 2052
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_d1.225
X-RAY DIFFRACTIONf_bond_d0.008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.32-2.40470.26941710.19991548154888
2.4047-2.5010.24741740.18971579157989
2.501-2.61480.2481890.19341620162091
2.6148-2.75270.26821810.19931676167694
2.7527-2.92510.28211800.20151688168895
2.9251-3.15090.30371930.22311729172996
3.1509-3.4680.24041930.20591758175897
3.468-3.96960.2281970.16731803180399
3.9696-5.00050.16612040.13661837183799
5.0005-49.13570.1852140.16891933193399
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)
11.4486-0.14460.12022.18772.23021.65580.04440.2661-0.1584-0.6127-0.03960.1436-0.40440.10380.02160.3507-0.0149-0.0160.3498-0.03230.3061-14.551218.1998-20.5435
21.98990.7559-0.45451.5075-0.7120.9275-0.0881-0.11640.07070.19070.20630.07570.02-0.2115-0.12410.26050.02530.02950.30810.0140.2403-9.445517.9326.5469
30.5683-0.45290.13570.5640.36670.19830.3049-0.0303-0.1891-0.16470.1527-0.00480.17860.0611-0.25140.6217-0.0751-0.07470.422-0.03650.2352-10.61622.4216-9.5804
40.9242-0.05390.41220.74190.01750.53370.25740.0155-0.20790.0760.21350.02830.47870.0234-0.32590.5485-0.0068-0.01790.3844-0.02840.283-9.14322.5535-5.7747
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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