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- PDB-5cc1: S425G Glucocorticoid receptor DNA binding domain - (+)GRE complex -

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Basic information

Entry
Database: PDB / ID: 5cc1
TitleS425G Glucocorticoid receptor DNA binding domain - (+)GRE complex
Components
  • DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*GP*AP*GP*TP*GP*TP*TP*CP*TP*G)-3')
  • DNA (5'-D(*TP*CP*AP*GP*AP*AP*CP*AP*CP*TP*CP*TP*GP*TP*TP*CP*TP*G)-3')
  • Glucocorticoid receptor
Keywordsdna binding protein/dna / DNA binding protein / 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 / 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 / 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 / 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 / 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 / sequence-specific double-stranded DNA binding / positive regulation of neuron apoptotic process / 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 / apoptotic process / synapse / regulation of DNA-templated transcription / chromatin / 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 / identical protein binding / membrane / nucleus / cytoplasm / cytosol
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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.302 Å
AuthorsHudson, W.H. / Weikum, E.A. / Ortlund, E.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK095750 United States
American Heart Association14GRNT20460124 United States
American Heart Association13PRE16920012 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Distal substitutions drive divergent DNA specificity among paralogous transcription factors through subdivision of conformational space.
Authors: Hudson, W.H. / Kossmann, B.R. / de Vera, I.M. / Chuo, S.W. / Weikum, E.R. / Eick, G.N. / Thornton, J.W. / Ivanov, I.N. / Kojetin, D.J. / Ortlund, E.A.
History
DepositionJul 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 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
A: Glucocorticoid receptor
B: Glucocorticoid receptor
C: DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*GP*AP*GP*TP*GP*TP*TP*CP*TP*G)-3')
D: DNA (5'-D(*TP*CP*AP*GP*AP*AP*CP*AP*CP*TP*CP*TP*GP*TP*TP*CP*TP*G)-3')
W: Glucocorticoid receptor
X: Glucocorticoid receptor
Y: DNA (5'-D(*TP*CP*AP*GP*AP*AP*CP*AP*CP*TP*CP*TP*GP*TP*TP*CP*TP*G)-3')
Z: DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*GP*AP*GP*TP*GP*TP*TP*CP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,45716
Polymers72,9338
Non-polymers5238
Water36020
1
A: Glucocorticoid receptor
B: Glucocorticoid receptor
C: DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*GP*AP*GP*TP*GP*TP*TP*CP*TP*G)-3')
D: DNA (5'-D(*TP*CP*AP*GP*AP*AP*CP*AP*CP*TP*CP*TP*GP*TP*TP*CP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7288
Polymers36,4674
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-32 kcal/mol
Surface area13120 Å2
MethodPISA
2
W: Glucocorticoid receptor
X: Glucocorticoid receptor
Y: DNA (5'-D(*TP*CP*AP*GP*AP*AP*CP*AP*CP*TP*CP*TP*GP*TP*TP*CP*TP*G)-3')
Z: DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*GP*AP*GP*TP*GP*TP*TP*CP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7288
Polymers36,4674
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-33 kcal/mol
Surface area13020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.721, 39.122, 132.099
Angle α, β, γ (deg.)90.00, 101.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Glucocorticoid receptor / GR / Nuclear receptor subfamily 3 group C member 1


Mass: 12729.778 Da / Num. of mol.: 4 / Mutation: S425G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR3C1, GRL / Production host: Escherichia coli (E. coli) / References: UniProt: P04150
#2: DNA chain DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*GP*AP*GP*TP*GP*TP*TP*CP*TP*G)-3')


Mass: 5540.604 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*CP*AP*GP*AP*AP*CP*AP*CP*TP*CP*TP*GP*TP*TP*CP*TP*G)-3')


Mass: 5466.553 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.07 Å3/Da / Density % sol: 59.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, 20% PEG 8000, and 4% ethylene glycol

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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: 2.3→50 Å / Num. obs: 36884 / % possible obs: 94.2 % / Redundancy: 3.3 % / Net I/σ(I): 13.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SERGUIdata collection
HKL-2000data reduction
PHASERphasing
RefinementResolution: 2.302→32.407 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 50.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2791 1945 5.3 %
Rwork0.2446 --
obs0.2464 36667 91.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.302→32.407 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2268 1460 8 20 3756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013936
X-RAY DIFFRACTIONf_angle_d1.4095586
X-RAY DIFFRACTIONf_dihedral_angle_d24.5631588
X-RAY DIFFRACTIONf_chiral_restr0.058608
X-RAY DIFFRACTIONf_plane_restr0.009472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3021-2.35960.46011030.45161821X-RAY DIFFRACTION69
2.3596-2.42340.42861240.43412215X-RAY DIFFRACTION82
2.4234-2.49470.46731310.4232294X-RAY DIFFRACTION86
2.4947-2.57520.39481360.41042432X-RAY DIFFRACTION91
2.5752-2.66720.51911450.39912565X-RAY DIFFRACTION95
2.6672-2.77390.40391470.37152622X-RAY DIFFRACTION97
2.7739-2.90010.32151450.35652602X-RAY DIFFRACTION97
2.9001-3.05290.37761490.33572650X-RAY DIFFRACTION98
3.0529-3.2440.34891460.30182589X-RAY DIFFRACTION95
3.244-3.49420.26541380.26032541X-RAY DIFFRACTION94
3.4942-3.84530.26461450.22872582X-RAY DIFFRACTION95
3.8453-4.40050.23551460.18742614X-RAY DIFFRACTION95
4.4005-5.53970.23771490.17482671X-RAY DIFFRACTION96
5.5397-32.41010.16881410.15352524X-RAY DIFFRACTION88

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