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- PDB-5uc1: Structural Analysis of Glucocorticoid Receptor beta Ligand Bindin... -

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Basic information

Entry
Database: PDB / ID: 5uc1
TitleStructural Analysis of Glucocorticoid Receptor beta Ligand Binding Domain Complexed with Glucocorticoid Antagonist RU-486: Implication of Helix 12 in Antagonism
ComponentsGlucocorticoid receptor
KeywordsHORMONE RECEPTOR / Nuclear receptor
Function / homology
Function and homology information


regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / neuroinflammatory response / glucocorticoid metabolic process / mammary gland duct morphogenesis / microglia differentiation / maternal behavior / astrocyte differentiation / motor behavior ...regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / neuroinflammatory response / glucocorticoid metabolic process / mammary gland duct morphogenesis / microglia differentiation / maternal behavior / astrocyte differentiation / motor behavior / adrenal gland development / regulation of gluconeogenesis / estrogen response element binding / core promoter sequence-specific DNA binding / cellular response to transforming growth factor beta stimulus / TBP-class protein binding / cellular response to dexamethasone stimulus / synaptic transmission, glutamatergic / Hsp90 protein binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / spindle / nuclear receptor activity / positive regulation of neuron apoptotic process / chromatin organization / gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear speck / centrosome / synapse / protein kinase binding / protein-containing complex / mitochondrion / zinc ion binding / identical protein binding / membrane / cytosol
Similarity search - Function
Glucocorticoid receptor / Glucocorticoid receptor / : / Retinoid X Receptor / Retinoid X Receptor / 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 / : / Retinoid X Receptor / Retinoid X Receptor / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-486 / Glucocorticoid receptor
Similarity search - Component
Biological speciesHeterocephalus glaber (naked mole-rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.351 Å
AuthorsPedersen, L.C. / Min, J.
CitationJournal: Mol. Cell. Biol. / Year: 2018
Title: Probing Dominant Negative Behavior of Glucocorticoid Receptor beta through a Hybrid Structural and Biochemical Approach.
Authors: Min, J. / Perera, L. / Krahn, J.M. / Jewell, C.M. / Moon, A.F. / Cidlowski, J.A. / Pedersen, L.C.
History
DepositionDec 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,27719
Polymers51,2692
Non-polymers4,00717
Water34219
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9040 Å2
ΔGint-66 kcal/mol
Surface area18620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.361, 48.361, 385.802
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glucocorticoid receptor


Mass: 25634.705 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Heterocephalus glaber (naked mole-rat) / Gene: GW7_10599 / Production host: Escherichia coli (E. coli) / References: UniProt: G5AQS2*PLUS

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Non-polymers , 6 types, 36 molecules

#2: Chemical ChemComp-486 / 11-(4-DIMETHYLAMINO-PHENYL)-17-HYDROXY-13-METHYL-17-PROP-1-YNYL-1,2,6,7,8,11,12,13,14,15,16,17-DODEC AHYDRO-CYCLOPENTA[A]PHENANTHREN-3-ONE / RU-486 / MIFEPRISTONE


Mass: 429.594 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H35NO2 / Comment: medication*YM
#3: Chemical
ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS


Mass: 614.877 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 5.0 and 20 % MPD (v/v)

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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: Mar 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 20767 / % possible obs: 98 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 28.6
Reflection shellRmerge(I) obs: 0.453

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M2Z

1m2z


Resolution: 2.351→35.094 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.88
RfactorNum. reflection% reflection
Rfree0.2541 1030 4.98 %
Rwork0.2039 --
obs0.2063 20699 98.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 105.6 Å2 / Biso mean: 57.6788 Å2 / Biso min: 34.52 Å2
Refinement stepCycle: final / Resolution: 2.351→35.094 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3206 0 210 19 3435
Biso mean--60.42 52.9 -
Num. residues----410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073495
X-RAY DIFFRACTIONf_angle_d0.8734776
X-RAY DIFFRACTIONf_chiral_restr0.043570
X-RAY DIFFRACTIONf_plane_restr0.005554
X-RAY DIFFRACTIONf_dihedral_angle_d13.0162001
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3509-2.47490.36051360.30112575271189
2.4749-2.62990.30051470.2612845299299
2.6299-2.83280.31471520.229428703022100
2.8328-3.11780.30251510.230728202971100
3.1178-3.56850.26881500.214228553005100
3.5685-4.49450.24821430.179928633006100
4.4945-35.09780.2111510.18672841299299

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