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- PDB-3g99: GR DNA binding domain:Pal complex-9 -

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Basic information

Entry
Database: PDB / ID: 3g99
TitleGR DNA binding domain:Pal complex-9
Components
  • DNA (5'-D(*AP*AP*GP*AP*AP*CP*AP*TP*TP*TP*TP*GP*TP*TP*CP*T)-3')
  • DNA (5'-D(*TP*AP*GP*AP*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


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 / 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
BROMIDE ION / DNA / DNA (> 10) / Glucocorticoid receptor
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 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
A: Glucocorticoid receptor
B: Glucocorticoid receptor
D: DNA (5'-D(*TP*AP*GP*AP*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*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,18411
Polymers29,7184
Non-polymers4667
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-15 kcal/mol
Surface area11850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.774, 38.189, 97.064
Angle α, β, γ (deg.)90.00, 123.11, 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*AP*GP*AP*AP*CP*AP*AP*AP*AP*TP*GP*TP*TP*CP*T)-3')


Mass: 4905.229 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Glucocorticoid receptor binding site Pal bottom strand
#3: DNA chain DNA (5'-D(*AP*AP*GP*AP*AP*CP*AP*TP*TP*TP*TP*GP*TP*TP*CP*T)-3')


Mass: 4887.201 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Glucocorticoid receptor binding site Pal top strand

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Non-polymers , 4 types, 101 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: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 3.05 Å3/Da / Density % sol: 59.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50mM MES, pH 6.0, 100 KCl, 10mM MgCl2, 10% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1MES11
2KCl11
3MgCl211
4MES12
5KCl12
6MgCl212
7PEG 40012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115894 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 26, 2008
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115894 Å / Relative weight: 1
ReflectionResolution: 1.81→50 Å / Num. obs: 24846 / % possible obs: 73.8 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 33.095 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.052 / Net I/σ(I): 14.9
Reflection shellResolution: 1.81→1.87 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.633 / Mean I/σ(I) obs: 1.1 / Num. unique all: 334 / Rsym value: 0.489 / % possible all: 10

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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: 1.81→35.574 Å / SU ML: 1.73 / σ(F): 0.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2304 1842 8.27 %PHENIX - Automatic
Rwork0.1908 ---
obs0.1941 22269 66.44 %-
all-24846 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.125 Å2 / ksol: 0.384 e/Å3
Displacement parametersBiso mean: 68 Å2
Refinement stepCycle: LAST / Resolution: 1.81→35.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1169 649 13 94 1925
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_d1.528
X-RAY DIFFRACTIONf_bond_d0.014
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.81-1.86760.3712220.29812392398
1.8676-1.94230.3481620.290460460420
1.9423-2.03070.34571060.28561168116838
2.0307-2.13780.33521640.24811759175958
2.1378-2.27170.27192000.22712268226874
2.2717-2.4470.24462330.20082582258285
2.447-2.69320.25592490.20922738273889
2.6932-3.08270.24522520.22942878287893
3.0827-3.88320.23492750.19523026302697
3.8832-35.58070.19042790.15143165316599
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)
12.4714-0.2190.25591.81710.42771.46070.14340.0029-0.4807-0.0992-0.1502-0.2852-0.05470.15610.00180.1831-0.01340.02150.16530.0760.326612.458-15.802941.4089
22.20620.69580.01190.9058-0.18740.474-0.2420.45770.0417-0.35210.03260.3059-0.03040.07790.06440.38460.0027-0.10660.2426-0.04810.2333-3.5777-20.333920.0392
32.90371.4951-0.59552.11922.53232.4654-0.37440.8744-0.5686-0.72220.8346-0.2764-0.95680.6457-0.30750.5451-0.19530.10270.51790.03490.375617.3973-14.949222.9338
4-0.21191.44711.22622.76111.60482.3009-0.45561.1495-0.5167-0.76010.5732-0.4933-0.65640.8053-0.19180.4866-0.12220.12040.842-0.15950.306615.2612-17.752518.9426
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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