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- PDB-3bqd: Doubling the Size of the Glucocorticoid Receptor Ligand Binding P... -

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Basic information

Entry
Database: PDB / ID: 3bqd
TitleDoubling the Size of the Glucocorticoid Receptor Ligand Binding Pocket by Deacylcortivazol
Components
  • Glucocorticoid receptor
  • Nuclear receptor coactivator 1
KeywordsPROTEIN BINDING / GLUCOCORTICOID RECEPTOR / deacylcortivazol / SRC1 / nuclear receptor coactivator 1 isoform 1 / DIMER INTERFACE / HORMONE BINDING POCKET / CHARGE CLAMP / COACTIVATOR / Alternative initiation / Alternative splicing / Chromatin regulator / Cytoplasm / Disease mutation / DNA-binding / Lipid-binding / Metal-binding / Nucleus / Phosphoprotein / Polymorphism / Pseudohermaphroditism / Steroid-binding / Transcription / Transcription regulation / Ubl conjugation / Zinc / Zinc-finger / Acyltransferase / Chromosomal rearrangement / Proto-oncogene / Transferase
Function / homology
Function and homology information


Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / response to cortisol / steroid hormone binding / glucocorticoid metabolic process / PTK6 Expression / neuroinflammatory response / mammary gland duct morphogenesis / microglia differentiation ...Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / response to cortisol / steroid hormone binding / glucocorticoid metabolic process / PTK6 Expression / neuroinflammatory response / mammary gland duct morphogenesis / microglia differentiation / astrocyte differentiation / maternal behavior / labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / cellular response to glucocorticoid stimulus / motor behavior / adrenal gland development / regulation of gluconeogenesis / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / cellular response to steroid hormone stimulus / hypothalamus development / male mating behavior / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear receptor-mediated steroid hormone signaling pathway / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / nuclear retinoid X receptor binding / response to retinoic acid / progesterone receptor signaling pathway / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / histone H4K16 acetyltransferase activity / cellular response to hormone stimulus / core promoter sequence-specific DNA binding / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / Recycling of bile acids and salts / histone acetyltransferase / estrous cycle / cellular response to transforming growth factor beta stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / estrogen receptor signaling pathway / positive regulation of adipose tissue development / steroid binding / : / lactation / Regulation of lipid metabolism by PPARalpha / TBP-class protein binding / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / positive regulation of neuron differentiation / cerebellum development / cellular response to dexamethasone stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Activation of gene expression by SREBF (SREBP) / hippocampus development / response to progesterone / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / nuclear estrogen receptor binding / synaptic transmission, glutamatergic / chromosome segregation / SUMOylation of intracellular receptors / Hsp90 protein binding / promoter-specific chromatin binding / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / positive regulation of miRNA transcription / response to wounding / DNA-binding transcription repressor activity, RNA polymerase II-specific / spindle / RNA polymerase II transcription regulator complex / nuclear receptor activity
Similarity search - Function
Glucocorticoid receptor / Glucocorticoid receptor / Nuclear receptor coactivator 1 / 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 ...Glucocorticoid receptor / Glucocorticoid receptor / Nuclear receptor coactivator 1 / 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 / Nuclear receptor coactivators bHLH domain / : / 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 / Double treble clef zinc finger, C4 type / 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-DAY / Glucocorticoid receptor / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsXu, H.E.
CitationJournal: Mol.Cell.Biol. / Year: 2008
Title: Doubling the size of the glucocorticoid receptor ligand binding pocket by deacylcortivazol.
Authors: Suino-Powell, K. / Xu, Y. / Zhang, C. / Tao, Y.G. / Tolbert, W.D. / Simons, S.S. / Xu, H.E.
History
DepositionDec 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 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 1.3Aug 30, 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: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5773
Polymers31,0882
Non-polymers4891
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.800, 93.800, 130.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

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


Mass: 29587.412 Da / Num. of mol.: 1
Fragment: glucocorticoid receptor ligand binding domain (residues 525-777)
Mutation: F602S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR3C1, GRL / Plasmid: pET24 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04150
#2: Protein/peptide Nuclear receptor coactivator 1 / NCoA-1 / Steroid receptor coactivator 1 / SRC-1 / RIP160 / Protein Hin-2 / Renal carcinoma antigen NY-REN-52


Mass: 1500.715 Da / Num. of mol.: 1
Fragment: nuclear receptor coactivator 1 isoform 1 coactivator motif (residues 739-751)
Source method: obtained synthetically / Details: synthetic peptide derived from gene sequence / References: UniProt: Q15788, histone acetyltransferase
#3: Chemical ChemComp-DAY / 1-[(1R,2R,3aS,3bS,10aR,10bS,11S,12aS)-1,11-dihydroxy-2,5,10a,12a-tetramethyl-7-phenyl-1,2,3,3a,3b,7,10,10a,10b,11,12,12a-dodecahydrocyclopenta[5,6]naphtho[1,2-f]indazol-1-yl]-2-hydroxyethanone / Deacylcortivazol / 11beta,17,21-Trihydroxy-6,16alpha-dimethyl-2'-phenyl-2'H-pregna-2,4,6-trieno(3,2-c)pyrazol-20-one / 2'H-Pregna-2,4,6-trieno(3,2-c)pyrazol-20-one / 11,17,21-trihydroxy-6,16-dimethyl-2'-phenyl-(11beta,16alpha)-(9CI) / 6,16A-DIMETHYLPREGNA-4,6-DIENE-11B,17A,21-TRIOL-20-ONE-2'-PHENYL-(3,2-C)- PYRAZO


Mass: 488.618 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H36N2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.3 M ammonium sulfate, 100 mM Tris, 8% glycerol, 3 mM n-hexadecyl-beta-maltoside, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 30, 2005 / Details: monochromator Si 1 1 1
RadiationMonochromator: Si 1 1 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 22367 / Num. obs: 20243 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 35.1 Å2 / Rsym value: 9.9 / Net I/σ(I): 32.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1M2Z

1m2z


Resolution: 2.5→40.6 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 98101 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1583 7.8 %RANDOM
Rwork0.231 ---
obs0.231 20243 90.2 %-
all-22437 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.1975 Å2 / ksol: 0.334263 e/Å3
Displacement parametersBiso mean: 73.9 Å2
Baniso -1Baniso -2Baniso -3
1-18.17 Å220.47 Å20 Å2
2--18.17 Å20 Å2
3----36.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.72 Å0.78 Å
Refinement stepCycle: LAST / Resolution: 2.5→40.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2149 0 36 63 2248
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.475 186 7.2 %
Rwork0.483 2405 -
obs--69.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3dac.pardac.top

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