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- PDB-3fyl: GR DNA binding domain:CGT complex -

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Basic information

Entry
Database: PDB / ID: 3fyl
TitleGR DNA binding domain:CGT complex
Components
  • DNA (5'-D(*AP*AP*GP*AP*AP*CP*AP*TP*TP*TP*TP*GP*TP*CP*CP*G)-3')
  • DNA (5'-D(*TP*CP*GP*GP*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 / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / negative regulation of synaptic plasticity / response to inactivity / negative regulation of long-term synaptic depression / nuclear receptor-mediated glucocorticoid signaling pathway / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity ...nuclear receptor-mediated corticosteroid signaling pathway / positive regulation of nuclear receptor-mediated glucocorticoid signaling pathway / muscle atrophy / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / negative regulation of synaptic plasticity / response to inactivity / negative regulation of long-term synaptic depression / nuclear receptor-mediated glucocorticoid signaling pathway / 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 / hormone binding / neuroinflammatory response / mammary gland duct morphogenesis / microglia differentiation / cellular response to magnesium ion / astrocyte differentiation / maternal behavior / response to arsenic-containing substance / negative regulation of vascular permeability / positive regulation of glutamate secretion / cellular response to glucocorticoid stimulus / motor behavior / response to corticosterone / positive regulation of dendritic spine development / regulation of gluconeogenesis / adrenal gland development / 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 / steroid binding / heat shock protein binding / TBP-class protein binding / Hsp70 protein binding / cellular response to dexamethasone stimulus / transcription initiation-coupled chromatin remodeling / response to activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / synaptic transmission, glutamatergic / female pregnancy / response to insulin / lung development / Hsp90 protein binding / receptor tyrosine kinase binding / positive regulation of miRNA transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / spindle / response to calcium ion / nuclear receptor activity / circadian rhythm / sequence-specific double-stranded DNA binding / positive regulation of neuron apoptotic process / regulation of cell population proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / protein-containing complex assembly / double-stranded DNA binding / 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 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: 1.63 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
DepositionJan 22, 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
C: DNA (5'-D(*AP*AP*GP*AP*AP*CP*AP*TP*TP*TP*TP*GP*TP*CP*CP*G)-3')
D: DNA (5'-D(*TP*CP*GP*GP*AP*CP*AP*AP*AP*AP*TP*GP*TP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0449
Polymers29,7204
Non-polymers3245
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-20 kcal/mol
Surface area12130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.445, 37.770, 96.679
Angle α, β, γ (deg.)90.00, 123.50, 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 CD

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


Mass: 4897.203 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Glucocorticoid receptor binding site - Cgt top strand
#3: DNA chain DNA (5'-D(*TP*CP*GP*GP*AP*CP*AP*AP*AP*AP*TP*GP*TP*TP*CP*T)-3')


Mass: 4897.203 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Glucocorticoid receptor binding site - Cgt bottom strand

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Non-polymers , 3 types, 165 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.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 3.01 Å3/Da / Density % sol: 59.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 50mM Tris, pH 8.5, 100mM KCl, 10mM MgCL2, 30% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1Tris11
2KCl11
3MgCl211
4Tris12
5KCl12
6MgCl212
7PEG 40012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115889 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: 1.115889 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. all: 31824 / Num. obs: 31824 / % possible obs: 71.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.052 / Rsym value: 0.037 / Net I/σ(I): 19.5
Reflection shellResolution: 1.63→1.69 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 1.4 / Num. unique all: 528 / Rsym value: 0.396 / % possible all: 12.1

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→35.24 Å / SU ML: 1.57 / σ(F): 0.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2337 1844 6.29 %10% random
Rwork0.1955 ---
obs0.1979 29316 65.92 %-
all-29316 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.258 Å2 / ksol: 0.383 e/Å3
Refinement stepCycle: LAST / Resolution: 1.63→35.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1164 650 8 160 1982
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_d1.538
X-RAY DIFFRACTIONf_bond_d0.013
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.63-1.69010.4054240.285239439410
1.6901-1.75780.3005500.227874174118
1.7578-1.83780.2941800.24651211121129
1.8378-1.93470.28121410.23952010201049
1.9347-2.05590.27082000.22062996299672
2.0559-2.21460.20382540.20233744374490
2.2146-2.43740.21342590.19193908390894
2.4374-2.790.24532700.20854053405397
2.79-3.51460.23812720.20164116411698
3.5146-35.24830.22212940.17524299429999
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)
11.37850.30160.10811.4511-0.71970.96640.1276-0.0138-0.2898-0.0758-0.05290.16280.0009-0.1535-0.06270.11050.0165-0.03690.2513-0.03460.241920.0257-17.0566-0.1091
21.068-0.4796-0.59710.24810.33520.6391-0.1976-0.46990.10270.20180.1553-0.35120.11170.29560.04990.25980.0506-0.11020.4384-0.00330.222735.5343-21.030621.5348
32.944-1.11172.24932.5247-1.77312.7923-0.2508-0.7-0.51220.49860.58730.1556-0.897-1.0186-0.26780.35070.14520.02960.70330.04990.213514.4532-15.417217.8498
40.6666-2.1192.59452.1676-1.42.9629-0.217-1.0842-0.62180.40590.59870.2723-0.4037-0.9574-0.31850.3150.07390.00810.86090.16650.311316.3979-18.323621.5715
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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