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- PDB-3hq5: Progesterone Receptor bound to an Alkylpyrrolidine ligand. -

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Basic information

Entry
Database: PDB / ID: 3hq5
TitleProgesterone Receptor bound to an Alkylpyrrolidine ligand.
ComponentsProgesterone receptor
Keywordshormone binding protein / nuclear receptor / Progesterone Receptor / PR / Alternative splicing / Cytoplasm / DNA-binding / Isopeptide bond / Lipid-binding / Metal-binding / Nucleus / Phosphoprotein / Polymorphism / Receptor / Steroid-binding / Transcription / Transcription regulation / Ubl conjugation / Zinc / 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-GKK / Progesterone receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsMadauss, K.P. / Williams, S.P. / Washburn, D.G.
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
DepositionJun 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,46510
Polymers59,1092
Non-polymers1,3568
Water8,071448
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-68 kcal/mol
Surface area22270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.701, 64.441, 70.380
Angle α, β, γ (deg.)90.000, 96.510, 90.000
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: 29554.633 Da / Num. of mol.: 2 / Fragment: residues 678-933
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGR, NR3C3 / Production host: Escherichia coli (E. coli) / References: UniProt: P06401
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GKK / 2-chloro-4-{[(3S)-1-methylpyrrolidin-3-yl][2-(trifluoromethyl)benzyl]amino}benzonitrile


Mass: 393.833 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H19ClF3N3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.2 Å3/Da / Density % sol: 44.07 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20 % Peg 3350, 0.2M LiSO4, 0.1M Hepes 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 32216 / % possible obs: 99.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 14.594
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.452 / % possible all: 96.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.99 Å
Translation2.5 Å19.99 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
SCALEPACKdata scaling
PHASER1.3.2phasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→19.99 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.604 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.291 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23678 2114 7 %RANDOM
Rwork0.1976 ---
obs0.20036 27875 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.557 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20.09 Å2
2---0.05 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4009 0 86 448 4543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224184
X-RAY DIFFRACTIONr_bond_other_d0.0010.022829
X-RAY DIFFRACTIONr_angle_refined_deg1.1162.0015669
X-RAY DIFFRACTIONr_angle_other_deg1.09636951
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4125498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23924.32169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.70615768
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4661519
X-RAY DIFFRACTIONr_chiral_restr0.0580.2648
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024504
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02819
X-RAY DIFFRACTIONr_nbd_refined0.1830.2971
X-RAY DIFFRACTIONr_nbd_other0.1730.22948
X-RAY DIFFRACTIONr_nbtor_refined0.1720.22041
X-RAY DIFFRACTIONr_nbtor_other0.0860.21937
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2332
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2680.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5331.52765
X-RAY DIFFRACTIONr_mcbond_other0.0851.5997
X-RAY DIFFRACTIONr_mcangle_it0.80824058
X-RAY DIFFRACTIONr_scbond_it1.04731855
X-RAY DIFFRACTIONr_scangle_it1.4714.51611
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 150 -
Rwork0.318 1997 -
obs--100 %

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