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- PDB-3g8o: Progesterone Receptor with bound Pyrrolidine 1 -

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Basic information

Entry
Database: PDB / ID: 3g8o
TitleProgesterone Receptor with bound Pyrrolidine 1
ComponentsProgesterone receptor
KeywordsTRANSCRIPTION / Progesterone Receptor / Steroid Hormone Receptor / Nuclear Receptor / PR / progesterone / alpha helical sandwich / DNA-binding / Lipid-binding / Metal-binding / Nucleus / Phosphoprotein / Receptor / Steroid-binding / Transcription regulation / Zinc-finger
Function / homology
Function and homology information


glandular epithelial cell maturation / tertiary branching involved in mammary gland duct morphogenesis / ovulation from ovarian follicle / paracrine signaling / regulation of epithelial cell proliferation / nuclear steroid receptor activity / lung alveolus development / progesterone receptor signaling pathway / estrogen response element binding / intracellular steroid hormone receptor signaling pathway ...glandular epithelial cell maturation / tertiary branching involved in mammary gland duct morphogenesis / ovulation from ovarian follicle / paracrine signaling / regulation of epithelial cell proliferation / nuclear steroid receptor activity / lung alveolus development / progesterone receptor signaling pathway / estrogen response element binding / intracellular steroid hormone receptor signaling pathway / Nuclear signaling by ERBB4 / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / steroid binding / G protein-coupled receptor activity / SUMOylation of intracellular receptors / transcription coactivator binding / Nuclear Receptor transcription pathway / nuclear receptor activity / cell-cell signaling / ATPase binding / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / mitochondrial outer membrane / nucleic acid binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / signaling receptor binding / chromatin / positive regulation of gene expression / regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Progesterone receptor / Progesterone 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 ...Progesterone receptor / Progesterone 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-30X / Progesterone receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsThompson, S.K. / Washburn, D.G. / Madauss, K.P. / Williams, S.P. / Stewart, E.L.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2009
Title: Rational design of orally-active, pyrrolidine-based progesterone receptor partial agonists.
Authors: Thompson, S.K. / Washburn, D.G. / Frazee, J.S. / Madauss, K.P. / Hoang, T.H. / Lapinski, L. / Grygielko, E.T. / Glace, L.E. / Trizna, W. / Williams, S.P. / Duraiswami, C. / Bray, J.D. / Laping, N.J.
History
DepositionFeb 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
SupersessionApr 11, 2012ID: 3G8N
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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_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

Downloads & links

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Assembly

Deposited unit
A: Progesterone receptor
B: Progesterone receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3875
Polymers60,5572
Non-polymers8313
Water6,341352
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-21 kcal/mol
Surface area22470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.670, 64.208, 70.500
Angle α, β, γ (deg.)90.00, 96.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Progesterone receptor / / PR / Nuclear receptor subfamily 3 group C member 3


Mass: 30278.400 Da / Num. of mol.: 2 / Fragment: ligand binding domain
Source method: isolated from a genetically manipulated source
Details: N-terminal 6XHis-GST tag / Source: (gene. exp.) Homo sapiens (human) / Gene: NR3C3, PGR / Plasmid: pHis GST / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06401
#2: Chemical ChemComp-30X / N~2~-[4-cyano-3-(trifluoromethyl)phenyl]-N,N-dimethyl-N~2~-(2,2,2-trifluoroethyl)-L-alaninamide


Mass: 367.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H15F6N3O
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.14 Å3/Da / Density % sol: 42.62 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 7
Details: 0.1M Hepes, 0.2M Lithium Sulfate, 15% PEG3350, pH 7.0, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC / Detector: CCD / Date: Nov 1, 2004 / Details: Quantum 210
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 3.5 % / Av σ(I) over netI: 13.24 / Number: 136976 / Rmerge(I) obs: 0.076 / Χ2: 0.69 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 38672 / % possible obs: 95.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.095099.910.030.7863.7
3.254.0910010.0390.793.8
2.843.2510010.0660.7163.8
2.582.8410010.1090.6793.8
2.392.5810010.1430.6383.8
2.252.3999.810.1820.6743.7
2.142.2598.710.240.6753.5
2.052.1494.510.3160.6713.3
1.972.0587.510.380.5833
1.91.9773.210.4210.5852.6
ReflectionResolution: 1.9→50 Å / Num. obs: 38672 / % possible obs: 95.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.076 / Χ2: 0.69 / Net I/σ(I): 13.243
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.972.60.42129410.585173.2
1.97-2.0530.3835170.583187.5
2.05-2.143.30.31638430.671194.5
2.14-2.253.50.2439620.675198.7
2.25-2.393.70.18240710.674199.8
2.39-2.583.80.14340050.6381100
2.58-2.843.80.10940270.6791100
2.84-3.253.80.06640650.7161100
3.25-4.093.80.03940820.791100
4.09-503.70.0341590.786199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.329 / Cor.coef. Fo:Fc: 0.706 / Cor.coef. Io to Ic: 0.718
Highest resolutionLowest resolution
Translation3.5 Å10 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1A28

1a28


Resolution: 1.9→20 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.812 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 2688 6.6 %Random
Rwork0.204 ---
all0.204 40487 --
obs0.204 38617 95.4 %-
Displacement parametersBiso max: 68.2 Å2 / Biso mean: 25.96 Å2 / Biso min: 10.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.224 Å20 Å2-0.009 Å2
2---0.127 Å20 Å2
3----0.097 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3976 0 55 352 4383
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.139
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5309.par

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