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- PDB-3gn8: X-ray Crystal Structure of AncGR2 in Complex with Dexamethasone -

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Basic information

Entry
Database: PDB / ID: 3gn8
TitleX-ray Crystal Structure of AncGR2 in Complex with Dexamethasone
Components
  • Glucocorticoid receptor 2
  • Nuclear receptor coactivator 2
KeywordsHORMONE/HORMONE ACTIVATOR / nuclear receptor / GR2 / evolution / glucocorticoid receptor / dexamethasone / cortisol / Activator / Nucleus / Phosphoprotein / Polymorphism / Transcription / Transcription regulation / HORMONE-HORMONE ACTIVATOR COMPLEX
Function / homology
Function and homology information


RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol ...RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / cellular response to hormone stimulus / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / response to progesterone / nuclear receptor binding / circadian regulation of gene expression / Heme signaling / mRNA transcription by RNA polymerase II / 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 / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / Circadian Clock / HATs acetylate histones / Estrogen-dependent gene expression / transcription regulator complex / transcription coactivator activity / nuclear body / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / chromatin binding / regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
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 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 DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Retinoid X Receptor / Retinoid X Receptor / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DEXAMETHASONE / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsOrtlund, E.A.
CitationJournal: Nature / Year: 2009
Title: An epistatic ratchet constrains the direction of glucocorticoid receptor evolution
Authors: Bridgham, J.T. / Ortlund, E.A. / Thornton, J.W.
History
DepositionMar 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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 2
B: Glucocorticoid receptor 2
C: Nuclear receptor coactivator 2
E: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0876
Polymers62,3034
Non-polymers7852
Water2,774154
1
A: Glucocorticoid receptor 2
C: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5443
Polymers31,1512
Non-polymers3921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-8 kcal/mol
Surface area12350 Å2
MethodPISA
2
B: Glucocorticoid receptor 2
E: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5443
Polymers31,1512
Non-polymers3921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-8 kcal/mol
Surface area12410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.218, 104.218, 144.166
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Glucocorticoid receptor 2


Mass: 28702.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pMALCH10T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Protein/peptide Nuclear receptor coactivator 2 / NCoA-2 / Transcriptional intermediary factor 2 / hTIF2


Mass: 2448.833 Da / Num. of mol.: 2 / Fragment: sequence database residues 734-754 / Source method: obtained synthetically
Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN).
References: UniProt: Q15596
#3: Chemical ChemComp-DEX / DEXAMETHASONE / 9A-FLUORO-16BETA-METHYLPREDNISOLONE


Mass: 392.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H29FO5 / Comment: medication, antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 3.63 Å3/Da / Density % sol: 66.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.5-0.75M ammonium acetate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 19, 2008 / Details: Double Crystal Monochromator Si-220
RadiationMonochromator: Double Crystal Si-220 / 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: 30813 / Num. obs: 30813 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 52.2 Å2 / Rsym value: 0.115
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 5.2 / Num. unique all: 3879 / Rsym value: 0.44 / % possible all: 100

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2Q1H

2q1h


Resolution: 2.5→49.01 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.903 / SU B: 17.599 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25467 1550 5 %RANDOM
Rwork0.1959 ---
obs0.19888 29216 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.643 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20.19 Å20 Å2
2--0.38 Å20 Å2
3----0.57 Å2
Refine analyzeLuzzati d res low obs: 90.17 Å / Luzzati sigma a obs: 0.317 Å
Refinement stepCycle: LAST / Resolution: 2.5→49.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4213 0 56 154 4423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224362
X-RAY DIFFRACTIONr_angle_refined_deg1.43425908
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3125517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.80524.362188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.75315813
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8421522
X-RAY DIFFRACTIONr_chiral_restr0.1010.2665
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023182
X-RAY DIFFRACTIONr_nbd_refined0.2070.22072
X-RAY DIFFRACTIONr_nbtor_refined0.3140.23041
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2187
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.212
X-RAY DIFFRACTIONr_mcbond_it0.8951.52679
X-RAY DIFFRACTIONr_mcangle_it1.49924195
X-RAY DIFFRACTIONr_scbond_it3.97931927
X-RAY DIFFRACTIONr_scangle_it3.5074.51713
X-RAY DIFFRACTIONr_rigid_bond_restr4.1734606
X-RAY DIFFRACTIONr_sphericity_free3.8673154
X-RAY DIFFRACTIONr_sphericity_bonded2.40434270
LS refinement shellResolution: 2.5→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 103 -
Rwork0.269 2174 -
obs--100 %

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