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- PDB-3g6t: GR gamma DNA-binding domain:FKBP5 16bp complex-34 -

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Basic information

Entry
Database: PDB / ID: 3g6t
TitleGR gamma DNA-binding domain:FKBP5 16bp complex-34
Components
  • DNA (5'-D(*AP*AP*GP*AP*AP*CP*AP*GP*GP*GP*TP*GP*TP*TP*CP*T)-3')
  • DNA (5'-D(*TP*AP*GP*AP*AP*CP*AP*CP*CP*CP*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 / 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 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 / double-stranded DNA binding / protein-containing complex assembly / DNA-binding transcription activator activity, RNA polymerase II-specific / gene expression / dendritic spine / 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 / Resolution: 1.9 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 8, 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 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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*AP*GP*AP*AP*CP*AP*CP*CP*CP*TP*GP*TP*TP*CP*T)-3')
C: DNA (5'-D(*AP*AP*GP*AP*AP*CP*AP*GP*GP*GP*TP*GP*TP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2978
Polymers30,0354
Non-polymers2624
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-27 kcal/mol
Surface area12170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.693, 39.716, 95.228
Angle α, β, γ (deg.)90.00, 122.79, 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: 10119.951 Da / Num. of mol.: 2 / Fragment: UNP residues 440-525 / Mutation: insertion of Arg after G470
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
#2: DNA chain DNA (5'-D(*TP*AP*GP*AP*AP*CP*AP*CP*CP*CP*TP*GP*TP*TP*CP*T)-3')


Mass: 4833.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: FKBP5 bottom strand
#3: DNA chain DNA (5'-D(*AP*AP*GP*AP*AP*CP*AP*GP*GP*GP*TP*GP*TP*TP*CP*T)-3')


Mass: 4962.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: FKBP5 top 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


Mass: 18.015 Da / Num. of mol.: 103 / 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: 3.06 Å3/Da / Density % sol: 59.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50mM HEPES, pH 7.0, 100mM KCl, 10mM MgCl2, 5% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1Hepes11
2KCl11
3MgCl211
4Hepes12
5KCl12
6MgCl212
7PEG 40012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115799 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 31, 2007
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115799 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 26432 / % possible obs: 90.3 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 36.191 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.044 / Net I/σ(I): 32.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1282 / Rsym value: 0.26 / % possible all: 44.3

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Processing

Software
NameVersionClassification
Blu-IceICEdata collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.9→31.086 Å / SU ML: 1.59 / σ(F): 0.15 / Phase error: 22.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2142 1881 7.61 %
Rwork0.1788 --
obs0.1814 24730 84.43 %
all-26432 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.427 Å2 / ksol: 0.39 e/Å3
Refinement stepCycle: LAST / Resolution: 1.9→31.086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1158 650 4 103 1915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143036
X-RAY DIFFRACTIONf_angle_d1.4815263
X-RAY DIFFRACTIONf_dihedral_angle_d20.882896
X-RAY DIFFRACTIONf_chiral_restr0.115291
X-RAY DIFFRACTIONf_plane_restr0.006394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.96330.2549880.2223959X-RAY DIFFRACTION36
1.9633-2.04190.23141330.2391583X-RAY DIFFRACTION59
2.0419-2.13490.25081760.21352126X-RAY DIFFRACTION79
2.1349-2.24740.23512030.19322389X-RAY DIFFRACTION89
2.2474-2.38810.20651880.1662507X-RAY DIFFRACTION93
2.3881-2.57240.18682070.16272576X-RAY DIFFRACTION96
2.5724-2.83120.21732230.17632632X-RAY DIFFRACTION97
2.8312-3.24050.22022120.1842678X-RAY DIFFRACTION98
3.2405-4.08120.1942270.16422679X-RAY DIFFRACTION98
4.0812-31.09010.20832240.16722719X-RAY DIFFRACTION97
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined3.74310.04160.49850.9836-0.71610.85430.06860.0236-0.4420.0796-0.07980.1007-0.0607-0.0845-0.00550.30710.0120.02210.2684-0.08270.3916-15.6536-15.3726-19.0056
23.7223-0.20390.18272.2738-1.1599-1.8788-0.1926-1.1772-0.24120.47530.0618-0.2696-0.3236-0.29770.09890.48440.0299-0.10380.68030.03580.3222
35.7495-1.42770.58012.1993-1.58655.7226-0.55-1.2807-0.66660.64750.94070.2354-0.9506-0.3527-0.32520.51820.19340.04130.57220.02030.3077
46.1353-3.79636.25562.6584-2.76456.2857-0.6985-2.1273-0.46060.78020.77610.2717-1.262-1.3098-0.11450.43840.09950.06280.93010.12040.2048
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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