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- PDB-4udc: GR in complex with dexamethasone -

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Basic information

Entry
Database: PDB / ID: 4udc
TitleGR in complex with dexamethasone
Components
  • GLUCOCORTICOID RECEPTOR
  • NUCLEAR RECEPTOR COACTIVATOR 2
KeywordsSIGNALING PROTEIN / NUCLEAR HORMONE RECEPTOR / LIGAND COMPLEX / PEPTIDE 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 / mammary gland duct morphogenesis / microglia differentiation / 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 / mammary gland duct morphogenesis / microglia differentiation / maternal behavior / astrocyte differentiation / motor behavior / cellular response to glucocorticoid stimulus / adrenal gland development / cellular response to steroid hormone stimulus / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / regulation of gluconeogenesis / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / estrogen response element binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear receptor-mediated steroid hormone signaling pathway / core promoter sequence-specific DNA binding / Recycling of bile acids and salts / cellular response to hormone stimulus / cellular response to transforming growth factor beta stimulus / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of adipose tissue development / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / steroid binding / Regulation of lipid metabolism by PPARalpha / TBP-class protein binding / regulation of cellular response to insulin stimulus / cellular response to dexamethasone stimulus / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / synaptic transmission, glutamatergic / response to progesterone / nuclear receptor binding / chromosome segregation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / circadian regulation of gene expression / SUMOylation of intracellular receptors / Heme signaling / mRNA transcription by RNA polymerase II / Hsp90 protein binding / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / spindle / RNA polymerase II transcription regulator complex / nuclear receptor activity / Regulation of RUNX2 expression and activity / positive regulation of neuron apoptotic process / sequence-specific double-stranded DNA binding / Circadian Clock / chromatin organization / HATs acetylate histones / gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / Potential therapeutics for SARS / transcription coactivator activity / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear body / nuclear speck / mitochondrial matrix / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / cell division / negative regulation of DNA-templated transcription / centrosome / chromatin binding / synapse / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / apoptotic process / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II
Similarity search - Function
Glucocorticoid receptor / Glucocorticoid receptor / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator ...Glucocorticoid receptor / Glucocorticoid receptor / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / PAS domain / : / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / 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
DEXAMETHASONE / Glucocorticoid receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsEdman, K. / Hogner, A. / Hussein, A. / Bjursell, M. / Aagaard, A. / Backstrom, S. / Bodin, C. / Wissler, L. / Jellesmark-Jensen, T. / Cavallin, A. ...Edman, K. / Hogner, A. / Hussein, A. / Bjursell, M. / Aagaard, A. / Backstrom, S. / Bodin, C. / Wissler, L. / Jellesmark-Jensen, T. / Cavallin, A. / Karlsson, U. / Nilsson, E. / Lecina, D. / Takahashi, R. / Grebner, C. / Lepisto, M. / Guallar, V.
CitationJournal: Structure / Year: 2015
Title: Ligand Binding Mechanism in Steroid Receptors: From Conserved Plasticity to Differential Evolutionary Constraints.
Authors: Edman, K. / Hosseini, A. / Bjursell, M.K. / Aagaard, A. / Wissler, L. / Gunnarsson, A. / Kaminski, T. / Kohler, C. / Backstrom, S. / Jensen, T.J. / Cavallin, A. / Karlsson, U. / Nilsson, E. ...Authors: Edman, K. / Hosseini, A. / Bjursell, M.K. / Aagaard, A. / Wissler, L. / Gunnarsson, A. / Kaminski, T. / Kohler, C. / Backstrom, S. / Jensen, T.J. / Cavallin, A. / Karlsson, U. / Nilsson, E. / Lecina, D. / Takahashi, R. / Grebner, C. / Geschwindner, S. / Lepisto, M. / Hogner, A.C. / Guallar, V.
History
DepositionDec 9, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Dec 16, 2015Group: Database references
Revision 1.3Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: GLUCOCORTICOID RECEPTOR
B: NUCLEAR RECEPTOR COACTIVATOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8714
Polymers33,8642
Non-polymers1,0072
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-6.7 kcal/mol
Surface area13130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.660, 84.660, 105.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein GLUCOCORTICOID RECEPTOR / GR / NUCLEAR RECEPTOR SUBFAMILY 3 GROUP C MEMBER 1


Mass: 32155.072 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN, UNP RESIDUES 500-777 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC1 / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P04150
#2: Protein/peptide NUCLEAR RECEPTOR COACTIVATOR 2 / NCOA-2 / CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 75 / BHLHE75 / TRANSCRIPTIONAL INTERMEDIARY FACTOR ...NCOA-2 / CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 75 / BHLHE75 / TRANSCRIPTIONAL INTERMEDIARY FACTOR 2 / HTIF2 / NCOA2


Mass: 1708.931 Da / Num. of mol.: 1 / Fragment: RESIDUES 740-753 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q15596
#3: Chemical ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS


Mass: 614.877 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#4: Chemical ChemComp-DEX / DEXAMETHASONE / 9A-FLUORO-16BETA-METHYLPREDNISOLONE


Mass: 392.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H29FO5 / Comment: medication, antibiotic*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 3.36 Å3/Da / Density % sol: 63.4 % / Description: NONE
Crystal growpH: 7.5
Details: 10% PEG8000, 10% ETHYLENE GLYCOL, 0.1 M HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.94
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 19, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 2.5→31.8 Å / Num. obs: 15574 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 54.81 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.8
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.6 / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M2Z

1m2z


Resolution: 2.5→31.81 Å / Cor.coef. Fo:Fc: 0.9135 / Cor.coef. Fo:Fc free: 0.8989 / SU R Cruickshank DPI: 0.312 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.322 / SU Rfree Blow DPI: 0.242 / SU Rfree Cruickshank DPI: 0.241
RfactorNum. reflection% reflectionSelection details
Rfree0.2528 778 5 %RANDOM
Rwork0.21 ---
obs0.2121 15559 99.43 %-
Displacement parametersBiso mean: 49.74 Å2
Baniso -1Baniso -2Baniso -3
1--8.8303 Å20 Å20 Å2
2---8.8303 Å20 Å2
3---17.6606 Å2
Refine analyzeLuzzati coordinate error obs: 0.338 Å
Refinement stepCycle: LAST / Resolution: 2.5→31.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2133 0 64 83 2280
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012247HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.123058HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d807SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes58HARMONIC2
X-RAY DIFFRACTIONt_gen_planes307HARMONIC5
X-RAY DIFFRACTIONt_it2247HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.51
X-RAY DIFFRACTIONt_other_torsion18.07
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion298SEMIHARMONIC5
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_contact2705SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.67 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3501 152 5.52 %
Rwork0.2986 2602 -
all0.3015 2754 -
obs--99.43 %

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