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- PDB-4lsj: Crystal Structure of the Glucocorticoid Receptor Ligand Binding D... -

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Basic information

Entry
Database: PDB / ID: 4lsj
TitleCrystal Structure of the Glucocorticoid Receptor Ligand Binding Domain Bound to a Dibenzoxapine Sulfonamide
Components
  • D30 peptide
  • Glucocorticoid receptor
KeywordsTRANSCRIPTION / nuclear hormone receptor
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 / 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 ...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-LSJ / Glucocorticoid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsCarson, M. / Luz, J.G. / Clawson, D. / Coghlan, M.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Glucocorticoid receptor modulators informed by crystallography lead to a new rationale for receptor selectivity, function, and implications for structure-based design.
Authors: Carson, M.W. / Luz, J.G. / Suen, C. / Montrose, C. / Zink, R. / Ruan, X. / Cheng, C. / Cole, H. / Adrian, M.D. / Kohlman, D.T. / Mabry, T. / Snyder, N. / Condon, B. / Maletic, M. / Clawson, ...Authors: Carson, M.W. / Luz, J.G. / Suen, C. / Montrose, C. / Zink, R. / Ruan, X. / Cheng, C. / Cole, H. / Adrian, M.D. / Kohlman, D.T. / Mabry, T. / Snyder, N. / Condon, B. / Maletic, M. / Clawson, D. / Pustilnik, A. / Coghlan, M.J.
History
DepositionJul 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Glucocorticoid receptor
B: D30 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3894
Polymers31,5182
Non-polymers8712
Water90150
1
A: Glucocorticoid receptor
B: D30 peptide
hetero molecules

A: Glucocorticoid receptor
B: D30 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7778
Polymers63,0354
Non-polymers1,7424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7480 Å2
ΔGint-59 kcal/mol
Surface area24090 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-10 kcal/mol
Surface area14700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.9620, 139.3980, 48.0680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 29942.820 Da / Num. of mol.: 1 / Fragment: Steroid-binding region, residues 522-777 / Mutation: F602Y, C638G
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: Protein/peptide D30 peptide


Mass: 1574.800 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: D30 synthetic peptide
#3: Chemical ChemComp-LSJ / N-{3-[(1Z)-1-(10-methoxydibenzo[b,e]oxepin-11(6H)-ylidene)propyl]phenyl}methanesulfonamide


Mass: 435.535 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H25NO4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.07 Å3/Da / Density % sol: 40.55 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M bis-tris propane pH 5.5, 0.3 M Magnesium Formate, VAPOR DIFFUSION, SITTING DROP, temperature 294.15K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD
RadiationMonochromator: Kohzu HLD-4 Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.35→139.4 Å / Num. obs: 11516 / Redundancy: 6.9 % / Biso Wilson estimate: 36.68 Å2
Reflection shellResolution: 2.35→2.48 Å / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.9.5refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→25.35 Å / Cor.coef. Fo:Fc: 0.9303 / Cor.coef. Fo:Fc free: 0.8967 / SU R Cruickshank DPI: 0.407 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2358 1008 8.79 %RANDOM
Rwork0.1799 ---
obs0.1847 11472 99.71 %-
Displacement parametersBiso mean: 36.74 Å2
Baniso -1Baniso -2Baniso -3
1--2.5199 Å20 Å20 Å2
2--9.0277 Å20 Å2
3----6.5078 Å2
Refine analyzeLuzzati coordinate error obs: 0.248 Å
Refinement stepCycle: LAST / Resolution: 2.35→25.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2065 0 62 50 2177
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012262HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.153069HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d779SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes70HARMONIC2
X-RAY DIFFRACTIONt_gen_planes321HARMONIC5
X-RAY DIFFRACTIONt_it2262HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.73
X-RAY DIFFRACTIONt_other_torsion20.63
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion281SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2737SEMIHARMONIC4
LS refinement shellResolution: 2.35→2.57 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2399 243 9.08 %
Rwork0.1838 2432 -
all0.1889 2675 -
obs--99.71 %

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