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- PDB-5e6d: Glucocorticoid receptor DNA binding domain - ICAM1 NF-kB response... -

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Basic information

Entry
Database: PDB / ID: 5e6d
TitleGlucocorticoid receptor DNA binding domain - ICAM1 NF-kB response element complex
Components
  • DNA (5'-D(*GP*CP*TP*CP*CP*GP*GP*AP*AP*TP*TP*TP*CP*CP*AP*A)-3')
  • DNA (5'-D(*TP*TP*GP*GP*AP*AP*AP*TP*TP*CP*CP*GP*GP*AP*GP*C)-3')
  • Glucocorticoid receptor
Keywordsdna binding protein/dna / DNA binding proteins / dna binding protein-dna complex
Function / homology
Function and homology information


Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / PTK6 Expression / glucocorticoid metabolic process / neuroinflammatory response / microglia differentiation / maternal behavior / mammary gland duct morphogenesis ...Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / PTK6 Expression / glucocorticoid metabolic process / neuroinflammatory response / microglia differentiation / maternal behavior / mammary gland duct morphogenesis / nucleus localization / astrocyte differentiation / cellular response to glucocorticoid stimulus / motor behavior / regulation of gluconeogenesis / adrenal gland development / cellular response to steroid hormone stimulus / estrogen response element binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / intracellular steroid hormone receptor signaling pathway / core promoter sequence-specific DNA binding / cellular response to transforming growth factor beta stimulus / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / TBP-class protein binding / steroid binding / cellular response to dexamethasone stimulus / synaptic transmission, glutamatergic / chromosome segregation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Hsp90 protein binding / SUMOylation of intracellular receptors / spindle / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / Nuclear Receptor transcription pathway / Regulation of RUNX2 expression and activity / positive regulation of neuron apoptotic process / nuclear receptor activity / Circadian Clock / sequence-specific double-stranded DNA binding / gene expression / chromatin organization / DNA-binding transcription activator activity, RNA polymerase II-specific / Potential therapeutics for SARS / DNA-binding transcription factor activity, RNA polymerase II-specific / mitochondrial matrix / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / cell division / centrosome / negative regulation of DNA-templated transcription / synapse / apoptotic process / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / zinc ion binding / nucleoplasm / 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
DNA / DNA (> 10) / Glucocorticoid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsHudson, W.H. / Rye, E.A. / Herbst, A.G. / Ortlund, E.A.
CitationJournal: Nat Commun / Year: 2018
Title: Cryptic glucocorticoid receptor-binding sites pervade genomic NF-kappa B response elements.
Authors: Hudson, W.H. / Vera, I.M.S. / Nwachukwu, J.C. / Weikum, E.R. / Herbst, A.G. / Yang, Q. / Bain, D.L. / Nettles, K.W. / Kojetin, D.J. / Ortlund, E.A.
History
DepositionOct 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.2Oct 24, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,5788
Polymers35,3164
Non-polymers2624
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-28 kcal/mol
Surface area12920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.059, 97.145, 104.018
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(*GP*CP*TP*CP*CP*GP*GP*AP*AP*TP*TP*TP*CP*CP*AP*A)-3')


Mass: 4858.167 Da / Num. of mol.: 1 / Fragment: unp residues 391-480 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA (5'-D(*TP*TP*GP*GP*AP*AP*AP*TP*TP*CP*CP*GP*GP*AP*GP*C)-3')


Mass: 4938.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein Glucocorticoid receptor / / GR / Nuclear receptor subfamily 3 group C member 1


Mass: 12759.804 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR3C1, GRL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P04150
#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 / Water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 7.7, 3% ethylene glycol, 10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.17→50 Å / Num. obs: 21692 / % possible obs: 96.6 % / Redundancy: 5.1 % / Net I/σ(I): 16.2
Reflection shellResolution: 2.17→2.25 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1.8 / % possible all: 91.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SERGUIdata collection
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.4→32.655 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2835 789 5 %
Rwork0.2569 --
obs0.2584 15770 97.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→32.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1113 650 4 19 1786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121872
X-RAY DIFFRACTIONf_angle_d1.2882649
X-RAY DIFFRACTIONf_dihedral_angle_d24.233742
X-RAY DIFFRACTIONf_chiral_restr0.052287
X-RAY DIFFRACTIONf_plane_restr0.006227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3998-2.55010.34421300.34512435X-RAY DIFFRACTION97
2.5501-2.74690.4051360.31962496X-RAY DIFFRACTION100
2.7469-3.02310.3581320.33612526X-RAY DIFFRACTION100
3.0231-3.46020.34251290.29412481X-RAY DIFFRACTION98
3.4602-4.35780.27591270.24982443X-RAY DIFFRACTION95
4.3578-32.6580.22771350.2142600X-RAY DIFFRACTION96

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