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- PDB-3h52: Crystal structure of the antagonist form of human glucocorticoid ... -

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Basic information

Entry
Database: PDB / ID: 3h52
TitleCrystal structure of the antagonist form of human glucocorticoid receptor
Components
  • Glucocorticoid receptor
  • Nuclear receptor corepressor 1
KeywordsHORMONE RECEPTOR / PROTEIN-LIGAND COMPLEX / NUCLEAR RECEPTOR / PEPTIDE COMPLEX / HORMONE RECEPTOR 3
Function / homology
Function and homology information


NR1D1 (REV-ERBA) represses gene expression / Loss of MECP2 binding ability to the NCoR/SMRT complex / Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / negative regulation of androgen receptor signaling pathway / steroid hormone binding / PTK6 Expression / neuroinflammatory response / glucocorticoid metabolic process ...NR1D1 (REV-ERBA) represses gene expression / Loss of MECP2 binding ability to the NCoR/SMRT complex / Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / negative regulation of androgen receptor signaling pathway / steroid hormone binding / PTK6 Expression / neuroinflammatory response / glucocorticoid metabolic process / microglia differentiation / mammary gland duct morphogenesis / maternal behavior / negative regulation of JNK cascade / astrocyte differentiation / negative regulation of glycolytic process / cellular response to glucocorticoid stimulus / motor behavior / nuclear thyroid hormone receptor binding / regulation of gluconeogenesis / adrenal gland development / cellular response to steroid hormone stimulus / negative regulation of fatty acid metabolic process / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Notch-HLH transcription pathway / locomotor rhythm / histone deacetylase complex / Regulation of MECP2 expression and activity / spindle assembly / 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 / Nuclear signaling by ERBB4 / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / 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 / transcription repressor complex / steroid binding / Regulation of lipid metabolism by PPARalpha / cellular response to dexamethasone stimulus / negative regulation of miRNA transcription / synaptic transmission, glutamatergic / chromosome segregation / HDACs deacetylate histones / nuclear receptor binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Hsp90 protein binding / Heme signaling / SUMOylation of intracellular receptors / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / NOTCH1 Intracellular Domain Regulates Transcription / mitotic spindle / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / histone deacetylase binding / Transcriptional regulation of white adipocyte differentiation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Nuclear Receptor transcription pathway / spindle / transcription corepressor activity / 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 / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / transcription cis-regulatory region binding / 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
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / N-CoR, GPS2-interacting domain / G-protein pathway suppressor 2-interacting domain / Glucocorticoid receptor / Glucocorticoid receptor / SANT domain profile. / SANT domain / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / N-CoR, GPS2-interacting domain / G-protein pathway suppressor 2-interacting domain / Glucocorticoid receptor / Glucocorticoid receptor / SANT domain profile. / SANT domain / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Retinoid X Receptor / Retinoid X Receptor / Helix non-globular / Homeobox-like domain superfamily / Special / 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 / Nuclear receptor corepressor 1 / Glucocorticoid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSchoch, G.A. / Benz, J. / D'Arcy, B. / Stihle, M. / Burger, D. / Thoma, R. / Ruf, A.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Molecular switch in the glucocorticoid receptor: active and passive antagonist conformations
Authors: Schoch, G.A. / D'Arcy, B. / Stihle, M. / Burger, D. / Bar, D. / Benz, J. / Thoma, R. / Ruf, A.
History
DepositionApr 21, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 5, 2014Group: Database references / Refinement description
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucocorticoid receptor
B: Glucocorticoid receptor
C: Glucocorticoid receptor
D: Glucocorticoid receptor
N: Nuclear receptor corepressor 1
M: Nuclear receptor corepressor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,17611
Polymers121,3656
Non-polymers1,8105
Water48627
1
A: Glucocorticoid receptor
D: Glucocorticoid receptor
N: Nuclear receptor corepressor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5425
Polymers60,6833
Non-polymers8592
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-52 kcal/mol
Surface area24410 Å2
MethodPISA
2
B: Glucocorticoid receptor
C: Glucocorticoid receptor
M: Nuclear receptor corepressor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6346
Polymers60,6833
Non-polymers9513
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7550 Å2
ΔGint-47 kcal/mol
Surface area24350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.530, 99.530, 252.430
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsFOUR COPIES OF THE RECEPTOR IN ASU. TWO PAIRS OF HOMODIMERS OF THE RECEPTOR ARE INVOLVED IN A PROPER DOMAIN SWAP INVOLVING THE N-TERMINAL 527-553 AMINO ACIDS. NO EVIDENCE THAT THIS HOMODIMER IS BIOLOGICALLY RELEVANT. THE INTERACTION FORMED BETWEEN RECEPTOR AND NCOR PEPTIDE IS BIOLOGICALLY RELEVANT.

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Components

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


Mass: 29315.096 Da / Num. of mol.: 4 / Fragment: Steroid-binding domain, UNP residues 528-777 / Mutation: F602S,C638D,W712S, E684A, E688A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P04150
#2: Protein/peptide Nuclear receptor corepressor 1 / N-CoR1 / N-CoR


Mass: 2052.354 Da / Num. of mol.: 2 / Fragment: CORNR box 3, UNP residues 2258-2276 / Source method: obtained synthetically / Details: synthetic peptide / References: UniProt: O75376
#3: 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.: 4 / Source method: obtained synthetically / Formula: C29H35NO2 / Comment: medication*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.97 Å3/Da / Density % sol: 58.64 %
Crystal growMethod: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 19, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→43.1 Å / Num. obs: 36561 / % possible obs: 99.7 % / Redundancy: 5.24 % / Biso Wilson estimate: 70.2 Å2 / Rmerge(I) obs: 0.118 / Rsym value: 0.108 / Net I/σ(I): 11.7
Reflection shellResolution: 2.8→2.97 Å / Redundancy: 4.17 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.9 / Num. unique all: 5762 / Rsym value: 0.612 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0088refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M2Z

1m2z


Resolution: 2.8→43.1 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.889 / SU B: 38.888 / SU ML: 0.335 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.104 / ESU R Free: 0.388 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28317 1830 5 %RANDOM
Rwork0.22557 ---
obs0.22838 34667 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.184 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.05 Å20 Å2
2---0.1 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.8→43.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7828 0 134 27 7989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228128
X-RAY DIFFRACTIONr_bond_other_d0.0010.025378
X-RAY DIFFRACTIONr_angle_refined_deg1.131.99411019
X-RAY DIFFRACTIONr_angle_other_deg0.856313165
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8665982
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97924.103329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.229151446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7131541
X-RAY DIFFRACTIONr_chiral_restr0.0590.21261
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028763
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021570
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3811.54944
X-RAY DIFFRACTIONr_mcbond_other0.0451.51987
X-RAY DIFFRACTIONr_mcangle_it0.72127927
X-RAY DIFFRACTIONr_scbond_it0.87133184
X-RAY DIFFRACTIONr_scangle_it1.4634.53092
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.801→2.874 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.446 114 -
Rwork0.339 2494 -
obs--97.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.9628.2803-3.345810.3193-3.46452.4381-0.0860.2216-0.44690.02350.0343-0.71040.24-0.11080.05170.069-0.0362-0.0150.38880.05660.2287-34.08834.509-66.038
21.5051-0.84683.29621.8509-1.624710.48540.0550.0539-0.0133-0.22640.03710.00790.2241-0.1776-0.09210.1153-0.10560.09820.1916-0.01550.2439-45.11829.059-23.527
310.25672.2873-3.82730.7925-1.36672.45790.2192-0.2110.12170.1181-0.13120.0523-0.25630.1667-0.0880.2744-0.0931-0.00440.134-0.06740.2142-12.4945.26-6.773
42.0873-1.2818-0.55662.37310.02770.213-0.32290.27180.2565-0.01470.3705-0.18040.1535-0.1971-0.04760.3368-0.31860.09520.42630.01120.2681-53.51620.496-29.557
51.44960.23830.23312.0496-0.70192.0116-0.0620.2495-0.1608-0.20720.07940.0210.4098-0.0322-0.01740.3445-0.19230.10360.1557-0.08410.1386-44.8348.914-31.847
63.17010.9841-0.57511.5682-0.21151.1091-0.0148-0.0674-0.27830.1256-0.083-0.29880.12540.24170.09790.1878-0.08910.0010.13570.00250.2129-9.27130.427-6.054
72.7273-0.6731.25312.7305-0.34622.6976-0.131-0.21250.35820.04450.02710.4227-0.4048-0.69350.10390.2197-0.04260.05710.3428-0.03310.2991-55.56939.603-22.51
82.5281.71930.0354.5927-0.05081.85790.0592-0.02160.38240.19370.05450.3906-0.1854-0.3026-0.11370.02670.03870.02110.40110.0730.2016-43.64245.91-65.009
95.8585-2.61257.6312.965-5.524912.4806-0.35740.58550.7495-0.045-0.8519-0.6135-0.15821.47721.20930.53670.01370.02790.5269-0.03080.5275-35.90315.701-47.907
1011.12990.9873-0.72040.4077-1.03393.0137-0.27470.8137-0.7449-0.0232-0.0024-0.11950.05870.15130.27710.2745-0.01150.03790.1545-0.09460.268-21.63321.88-16.753
113.52131.8818-0.28181.5982-2.42479.6792-0.2596-0.14810.3321-0.1799-0.03590.1156-0.37940.25870.29550.4287-0.1387-0.01740.30680.0070.3845-41.96749.703-17.87
129.4517-2.46510.17930.6642-2.772411.8348-0.6626-0.25710.1977-0.01740.0528-0.11920.4183-0.86470.60981.6911-0.25650.64161.4197-0.18550.9278-48.5944.424-47.577
135.7667-3.4095.375612.1326-3.18315.0136-0.48130.95360.5035-0.73050.03050.0773-0.470.90020.45080.3206-0.22550.0710.28520.04310.2987-34.66525.577-36.517
144.0155-5.36966.88297.1899-9.206511.80020.29730.35290.0678-0.4582-0.3863-0.09070.50230.58950.08910.7121-0.60660.30270.7948-0.12640.6593-17.8434.237-23.566
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A527 - 553
2X-RAY DIFFRACTION2B528 - 553
3X-RAY DIFFRACTION3C527 - 553
4X-RAY DIFFRACTION4D530 - 553
5X-RAY DIFFRACTION5A554 - 746
6X-RAY DIFFRACTION5A768 - 776
7X-RAY DIFFRACTION5A3
8X-RAY DIFFRACTION6B554 - 746
9X-RAY DIFFRACTION6B768 - 776
10X-RAY DIFFRACTION6B1
11X-RAY DIFFRACTION7C554 - 740
12X-RAY DIFFRACTION7C768 - 776
13X-RAY DIFFRACTION7C4
14X-RAY DIFFRACTION8D554 - 741
15X-RAY DIFFRACTION8D768 - 776
16X-RAY DIFFRACTION8D2
17X-RAY DIFFRACTION9A747 - 767
18X-RAY DIFFRACTION10B747 - 767
19X-RAY DIFFRACTION11C754 - 767
20X-RAY DIFFRACTION12D751 - 767
21X-RAY DIFFRACTION13N2260 - 2274
22X-RAY DIFFRACTION14M2265 - 2274

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