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- PDB-3g9i: GR DNA Binding domain: Pal complex-35 -

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Basic information

Entry
Database: PDB / ID: 3g9i
TitleGR DNA Binding domain: Pal complex-35
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


nuclear receptor-mediated corticosteroid signaling pathway / positive regulation of nuclear receptor-mediated glucocorticoid signaling pathway / muscle atrophy / negative regulation of synaptic plasticity / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to inactivity / nuclear receptor-mediated glucocorticoid signaling pathway / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / SUMOylation of intracellular receptors ...nuclear receptor-mediated corticosteroid signaling pathway / positive regulation of nuclear receptor-mediated glucocorticoid signaling pathway / muscle atrophy / negative regulation of synaptic plasticity / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to inactivity / nuclear receptor-mediated glucocorticoid signaling pathway / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / positive regulation of cell growth involved in cardiac muscle cell development / steroid hormone binding / response to mercury ion / hormone binding / glucocorticoid metabolic process / neuroinflammatory response / mammary gland duct morphogenesis / microglia differentiation / cellular response to magnesium ion / response to arsenic-containing substance / astrocyte differentiation / maternal behavior / negative regulation of vascular permeability / positive regulation of glutamate secretion / cellular response to glucocorticoid stimulus / motor behavior / positive regulation of dendritic spine development / response to corticosterone / adrenal gland development / regulation of gluconeogenesis / cellular response to steroid hormone stimulus / response to dexamethasone / androgen metabolic process / regulation of glucose metabolic process / estrogen response element binding / postsynaptic density, intracellular component / nuclear receptor-mediated steroid hormone signaling pathway / response to electrical stimulus / core promoter sequence-specific DNA binding / cellular response to transforming growth factor beta stimulus / heat shock protein binding / steroid binding / TBP-class protein binding / Hsp70 protein binding / transcription initiation-coupled chromatin remodeling / cellular response to dexamethasone stimulus / response to activity / synaptic transmission, glutamatergic / RNA polymerase II transcription regulatory region sequence-specific DNA binding / female pregnancy / response to insulin / lung development / Hsp90 protein binding / receptor tyrosine kinase binding / positive regulation of miRNA transcription / spindle / DNA-binding transcription repressor activity, RNA polymerase II-specific / response to calcium ion / circadian rhythm / nuclear receptor activity / sequence-specific double-stranded DNA binding / positive regulation of neuron apoptotic process / regulation of cell population proliferation / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / protein-containing complex assembly / gene expression / 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 / negative regulation of DNA-templated transcription / centrosome / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein-containing complex binding / negative regulation of apoptotic process / protein kinase binding / chromatin / 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 / nucleus / membrane / 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 / 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: 1.85 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)30,16611
Polymers29,7184
Non-polymers4487
Water2,954164
1
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

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)60,33222
Polymers59,4368
Non-polymers89614
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area12490 Å2
ΔGint-46 kcal/mol
Surface area24210 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-18 kcal/mol
Surface area12950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.513, 37.648, 95.448
Angle α, β, γ (deg.)90.00, 123.08, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-68-

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: 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: GR 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: GR binding site: Pal top strand

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Non-polymers , 3 types, 171 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.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.95 Å3/Da / Density % sol: 58.32 %
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
7PEG40012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115879 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 24, 2007
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115879 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 26375 / % possible obs: 87.7 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 28.562 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.047 / Net I/σ(I): 22
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 1.4 / Num. unique all: 1426 / Rsym value: 0.569 / % possible all: 48

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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: 1.85→48.814 Å / SU ML: 1.83 / σ(F): 0.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2013 1838 7.57 %PHENIX - automatic
Rwork0.1699 ---
obs0.1723 24291 80.74 %-
all-26375 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.562 Å2 / ksol: 0.404 e/Å3
Displacement parametersBiso mean: 54.51 Å2
Refinement stepCycle: LAST / Resolution: 1.85→48.814 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 650 16 164 2042
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_deg1.435
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 (%)
1.85-1.91620.3681850.28171021102137
1.9162-1.99290.25471240.24111486148654
1.9929-2.08360.24041510.21581884188468
2.0836-2.19350.25051920.18972265226583
2.1935-2.33090.19381950.17282428242887
2.3309-2.51090.23221920.15772499249990
2.5109-2.76350.212230.16082591259194
2.7635-3.16340.20732220.18472687268796
3.1634-3.98520.19232220.15422726272697
3.9852-48.83060.16392320.15182866286699
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)
12.00070.4552-0.73161.7045-0.2947-1.3214-0.25060.8637-0.0448-0.57210.20640.18630.1285-0.33380.01250.4476-0.0642-0.03950.5012-0.0170.2313-35.721611.6054-21.9032
21.8872-0.69670.3441.66690.67651.13450.10340.0154-0.2626-0.0389-0.0496-0.20030.05650.209-0.05510.1915-0.01040.01140.14270.03220.2892-19.052616.5011.2088
3-0.1142.74512.16572.06921.71533.6083-0.32191.1946-0.5977-0.32250.6136-0.3096-0.6771.0644-0.26140.2892-0.0680.06970.7872-0.18470.2859-16.375714.6167-21.6536
43.03181.3257-0.0321.91071.93473.4756-0.21550.848-0.6085-0.49730.617-0.2561-0.67180.8439-0.30950.374-0.14360.08130.5203-0.03980.2513-14.353317.5282-17.8073
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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