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- PDB-5e69: Glucocorticoid receptor DNA binding domain - IL8 NF-kB response e... -

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Basic information

Entry
Database: PDB / ID: 5.0E+69
TitleGlucocorticoid receptor DNA binding domain - IL8 NF-kB response element complex
Components
  • DNA (5'-D(*AP*TP*CP*GP*TP*GP*GP*AP*AP*TP*TP*TP*CP*CP*TP*C)-3')
  • DNA (5'-D(*GP*AP*GP*GP*AP*AP*AP*TP*TP*CP*CP*AP*CP*GP*AP*T)-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 / neuroinflammatory response / glucocorticoid metabolic process / microglia differentiation / mammary gland duct morphogenesis / maternal behavior ...Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / PTK6 Expression / neuroinflammatory response / glucocorticoid metabolic process / microglia differentiation / mammary gland duct morphogenesis / maternal behavior / astrocyte differentiation / cellular response to glucocorticoid stimulus / motor behavior / adrenal gland development / regulation of gluconeogenesis / cellular response to steroid hormone stimulus / estrogen response element binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / nuclear receptor-mediated steroid hormone 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 / steroid binding / TBP-class protein binding / cellular response to dexamethasone stimulus / synaptic transmission, glutamatergic / chromosome segregation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / Hsp90 protein binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / Nuclear Receptor transcription pathway / spindle / Regulation of RUNX2 expression and activity / nuclear receptor activity / positive regulation of neuron apoptotic process / sequence-specific double-stranded DNA binding / Circadian Clock / chromatin organization / gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / Potential therapeutics for SARS / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / mitochondrial matrix / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / cell division / negative regulation of DNA-templated transcription / centrosome / synapse / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / apoptotic process / 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 / identical protein binding / membrane / 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. ...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 / MOLECULAR REPLACEMENT / Resolution: 1.85 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 1.1Oct 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 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucocorticoid receptor
C: DNA (5'-D(*GP*AP*GP*GP*AP*AP*AP*TP*TP*CP*CP*AP*CP*GP*AP*T)-3')
D: DNA (5'-D(*AP*TP*CP*GP*TP*GP*GP*AP*AP*TP*TP*TP*CP*CP*TP*C)-3')
B: Glucocorticoid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5778
Polymers35,3154
Non-polymers2624
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-27 kcal/mol
Surface area12620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.165, 97.176, 103.265
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: Protein Glucocorticoid receptor / GR / Nuclear receptor subfamily 3 group C member 1


Mass: 12759.804 Da / Num. of mol.: 2 / Fragment: unp residues 391-480
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): BL-21 (DE3) PLYSS / References: UniProt: P04150
#2: DNA chain DNA (5'-D(*GP*AP*GP*GP*AP*AP*AP*TP*TP*CP*CP*AP*CP*GP*AP*T)-3')


Mass: 4931.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*AP*TP*CP*GP*TP*GP*GP*AP*AP*TP*TP*TP*CP*CP*TP*C)-3')


Mass: 4864.164 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#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.: 96 / 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: 2.78 Å3/Da / Density % sol: 55.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.5, 7.5% glycerol, 22% PEG 20000

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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: Dec 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→34.27 Å / Num. obs: 30412 / % possible obs: 88.4 % / Redundancy: 4.4 % / Net I/σ(I): 14
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.8 / % possible all: 74.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SERGUIdata collection
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→34.267 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2418 1978 6.52 %Random selection
Rwork0.2197 ---
obs0.2212 30348 87.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→34.267 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1120 650 4 96 1870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071880
X-RAY DIFFRACTIONf_angle_d0.8522660
X-RAY DIFFRACTIONf_dihedral_angle_d21.94746
X-RAY DIFFRACTIONf_chiral_restr0.037288
X-RAY DIFFRACTIONf_plane_restr0.006228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8502-1.89650.35121130.34311518X-RAY DIFFRACTION68
1.8965-1.94780.41951240.36581853X-RAY DIFFRACTION81
1.9478-2.00510.33711360.31391970X-RAY DIFFRACTION88
2.0051-2.06980.27321450.29852007X-RAY DIFFRACTION88
2.0698-2.14380.34191410.27292083X-RAY DIFFRACTION92
2.1438-2.22960.29341520.25982154X-RAY DIFFRACTION94
2.2296-2.3310.29561480.26632131X-RAY DIFFRACTION93
2.331-2.45390.28971520.24322158X-RAY DIFFRACTION94
2.4539-2.60760.28741490.24022113X-RAY DIFFRACTION93
2.6076-2.80880.25841550.23652107X-RAY DIFFRACTION92
2.8088-3.09130.23241390.23552107X-RAY DIFFRACTION91
3.0913-3.53830.24761390.21842090X-RAY DIFFRACTION89
3.5383-4.45630.21691480.19352067X-RAY DIFFRACTION88
4.4563-34.27320.18761370.17652012X-RAY DIFFRACTION81

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