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- PDB-3g6r: GR DNA binding domain:FKBP5 complex-52, 18bp -

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Basic information

Entry
Database: PDB / ID: 3g6r
TitleGR DNA binding domain:FKBP5 complex-52, 18bp
Components
  • DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*CP*CP*CP*TP*GP*TP*TP*CP*TP*G)-3')
  • DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*GP*GP*GP*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 / muscle atrophy / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / negative regulation of synaptic plasticity / positive regulation of nuclear receptor-mediated glucocorticoid signaling pathway / nuclear receptor-mediated glucocorticoid signaling pathway / response to inactivity / negative regulation of long-term synaptic depression / regulation of glucocorticoid biosynthetic process ...nuclear receptor-mediated corticosteroid signaling pathway / negative regulation of behavioral fear response / muscle atrophy / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / negative regulation of synaptic plasticity / positive regulation of nuclear receptor-mediated glucocorticoid signaling pathway / nuclear receptor-mediated glucocorticoid signaling pathway / response to inactivity / negative regulation of long-term synaptic depression / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / SUMOylation of intracellular receptors / positive regulation of cell growth involved in cardiac muscle cell development / steroid hormone binding / Nuclear Receptor transcription pathway / response to mercury ion / 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 / associative learning / androgen metabolic process / 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 / postsynaptic density, intracellular component / cellular response to transforming growth factor beta stimulus / 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 / synaptic transmission, glutamatergic / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Hsp90 protein binding / promoter-specific chromatin binding / female pregnancy / response to calcium ion / response to insulin / circadian rhythm / 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 / 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 / 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 transcription by RNA polymerase II / protein kinase binding / negative regulation of apoptotic process / regulation of DNA-templated transcription / 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: 2.3 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 1.3Sep 6, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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*GP*GP*GP*TP*GP*TP*TP*CP*TP*G)-3')
D: DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*CP*CP*CP*TP*GP*TP*TP*CP*TP*G)-3')
B: Glucocorticoid receptor
A: Glucocorticoid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1808
Polymers30,9194
Non-polymers2624
Water2,576143
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-24 kcal/mol
Surface area12980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.688, 101.310, 112.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 5556.603 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: FKBP5 binding site top strand 18bp
#2: DNA chain DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*CP*CP*CP*TP*GP*TP*TP*CP*TP*G)-3')


Mass: 5436.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: FKBP5 binding site bottom strand 18bp
#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: Grl, Nr3c1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: P06536
#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.: 143 / 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: 3.66 Å3/Da / Density % sol: 66.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50mM Na Cacodylate, pH 6.5, 2.25mM Spermine, 18mM MgCl2, 9% Isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1Cacodylate11
2Spermine11
3MgCl211
4Cacodylate12
5Spermine12
6MgCl212
7Isopropanol12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.282963 Å
DetectorType: ADSC QUANTUM Q315r / 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: 1.282963 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 19913 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 37.422 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.08 / Net I/σ(I): 19.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 1.88 / Num. unique all: 1322 / Rsym value: 0.394 / % possible all: 65

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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: PDB ENTRY 1GLU

1glu


Resolution: 2.3→49.195 Å / SU ML: 2.14 / σ(F): 0.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2382 1846 9.93 %PHENIX automatic
Rwork0.1873 ---
obs0.1923 18599 88.98 %-
all-19913 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.377 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso mean: 54.82 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.195 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1169 729 4 143 2045
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_d1.301
X-RAY DIFFRACTIONf_bond_d0.009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.3-2.38280.3332970.261194494451
2.3828-2.47820.28921470.24391333133371
2.4782-2.59090.28081700.21871562156285
2.5909-2.72750.26541860.21521699169992
2.7275-2.89840.28711970.20391781178195
2.8984-3.12210.24232020.19721818181897
3.1221-3.43630.24012010.17631806180697
3.4363-3.93330.21132090.15731885188599
3.9333-4.95480.18142140.142119211921100
4.9548-49.20610.2222230.178420042004100
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)
11.97870.1906-0.92941.5930.14210.9129-0.04010.1841-0.09-0.13080.1956-0.01510.2236-0.11050.00030.2305-0.02310.00360.2978-0.01290.35749.826817.8795-6.613
20.64820.28810.04451.4602-0.85391.07510.2899-0.2669-0.04660.7794-0.1809-0.0841-0.224-0.0452-0.00030.4063-0.0445-0.02880.35690.03520.394514.959318.095420.3441
30.49310.6385-0.00510.34610.02930.00740.31510.0139-0.18890.16330.0795-0.08430.5886-0.1042-0.00050.66090.0347-0.07640.40140.04240.333810.77332.33289.5112
40.78990.10670.26660.6367-0.02740.23080.1252-0.042-0.15460.11680.0727-0.01630.3901-0.00070.00010.5175-0.0098-0.03180.43170.02280.3639.28262.47885.6474
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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