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- PDB-3g6p: GR DNA binding domain:FKBP5 complex, 18bp -

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Basic information

Entry
Database: PDB / ID: 3g6p
TitleGR DNA binding domain:FKBP5 complex, 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 / 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 / positive regulation of cell growth involved in cardiac muscle cell development / SUMOylation of intracellular receptors / 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 / circadian rhythm / response to insulin / 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 / protein-containing complex assembly / double-stranded DNA binding / 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
ACETATE ION / DNA / DNA (> 10) / Glucocorticoid receptor
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.985 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 7, 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
C: DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*CP*CP*CP*TP*GP*TP*TP*CP*TP*G)-3')
D: DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*GP*GP*GP*TP*GP*TP*TP*CP*TP*G)-3')
A: Glucocorticoid receptor
B: Glucocorticoid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,35711
Polymers30,9194
Non-polymers4397
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-29 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.060, 100.110, 112.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 2 types, 2 molecules CD

#1: 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: GR binding site FKBP5 top strand
#2: 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: GR binding site FKBP5 bottom strand

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 3 types, 122 molecules

#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 3.55 Å3/Da / Density % sol: 65.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50mM Na cacodylate pH 6.0, 1mM Spermidine, 20mM MgCL2, 2mM CaCl2, 10% 1,5-hexanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1Cacodylate11
2CaCl211
3MgCl211
4Spermidine11
5Cacodylate12
6CaCl212
7MgCl212
81,5-hexanediol12
9Spermidine12

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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 Q315r / Detector: CCD / Date: Apr 10, 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: 1.98→50 Å / Num. all: 31363 / Num. obs: 30730 / % possible obs: 98 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 39.8 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.03
Reflection shellResolution: 1.98→2.04 Å / Rmerge(I) obs: 0.031 / Mean I/σ(I) obs: 0.38 / Num. unique all: 1892 / % possible all: 83.3

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GLU

1glu


Resolution: 1.985→28.694 Å / SU ML: -0 / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2389 2000 6.51 %
Rwork0.2138 --
obs0.2155 30728 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.541 Å2 / ksol: 0.352 e/Å3
Refinement stepCycle: LAST / Resolution: 1.985→28.694 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1185 729 13 115 2042
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_deg1.233
X-RAY DIFFRACTIONf_bond_d0.008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.985-2.05550.39921730.41982481248186
2.0555-2.13770.37281980.325728442844100
2.1377-2.2350.29862000.271928792879100
2.235-2.35280.28082010.231328822882100
2.3528-2.50010.25642010.22182894289499
2.5001-2.6930.28952010.215528942894100
2.693-2.96380.22742030.21252913291399
2.9638-3.39210.23192000.20192875287598
3.3921-4.27140.19082070.17822959295999
4.2714-28.69670.20822160.17813107310799
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)
10.73340.3596-0.30091.80880.97621.6279-0.0380.27990.0908-0.5860.15790.0262-0.3637-0.1467-0.1090.3963-0.0901-0.0090.3629-0.03150.368-13.943917.9333-20.7017
20.73690.79290.99521.2606-1.24532.2909-0.0208-0.209-0.11010.1010.34040.19840.014-0.4165-0.31680.23180.0320.04860.35360.08690.3791-8.964117.82417.3014
31.08-0.58390.9821-0.17090.4390.96250.41360.0346-0.3841-0.02780.1647-0.04850.85350.0151-0.46010.8908-0.137-0.11010.37810.01130.3781-10.86252.1497-9.2445
40.9274-0.83910.8375-0.15740.2650.58770.2236-0.0553-0.30050.25020.15780.10990.9482-0.217-0.24910.7831-0.0685-0.00970.4164-0.03340.3588-9.46832.3157-5.8382
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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