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- PDB-4apu: PR X-Ray structures in agonist conformations reveal two different... -

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Basic information

Entry
Database: PDB / ID: 4apu
TitlePR X-Ray structures in agonist conformations reveal two different mechanisms for partial agonism in 11beta-substituted steroids
ComponentsPROGESTERONE RECEPTOR
KeywordsTRANSCRIPTION / ASOPRISNIL / PARTIAL AGONIST
Function / homology
Function and homology information


glandular epithelial cell maturation / tertiary branching involved in mammary gland duct morphogenesis / ovulation from ovarian follicle / paracrine signaling / maintenance of protein location in nucleus / regulation of epithelial cell proliferation / nuclear steroid receptor activity / lung alveolus development / estrogen response element binding / progesterone receptor signaling pathway ...glandular epithelial cell maturation / tertiary branching involved in mammary gland duct morphogenesis / ovulation from ovarian follicle / paracrine signaling / maintenance of protein location in nucleus / regulation of epithelial cell proliferation / nuclear steroid receptor activity / lung alveolus development / estrogen response element binding / progesterone receptor signaling pathway / nuclear receptor-mediated steroid hormone 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 / 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 / regulation of DNA-templated transcription / positive regulation of gene expression / chromatin / 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. ...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-A2K / Chem-OR8 / Progesterone receptor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsLusher, S.J. / Raaijmakers, H.C.A. / Bosch, R. / Vu-Pham, D. / McGuire, R. / Oubrie, A. / de Vlieg, J.
CitationJournal: J. Biol. Chem. / Year: 2012
Title: X-ray structures of progesterone receptor ligand binding domain in its agonist state reveal differing mechanisms for mixed profiles of 11 beta-substituted steroids.
Authors: Lusher, S.J. / Raaijmakers, H.C. / Vu-Pham, D. / Kazemier, B. / Bosch, R. / McGuire, R. / Azevedo, R. / Hamersma, H. / Dechering, K. / Oubrie, A. / van Duin, M. / de Vlieg, J.
History
DepositionApr 6, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2012Group: Other
Revision 1.2Feb 7, 2018Group: Database references / Experimental preparation / Category: citation / citation_author / exptl_crystal
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _exptl_crystal.description
Revision 1.3Dec 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: PROGESTERONE RECEPTOR
B: PROGESTERONE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9315
Polymers59,9362
Non-polymers9953
Water2,900161
1
A: PROGESTERONE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4593
Polymers29,9681
Non-polymers4912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROGESTERONE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4722
Polymers29,9681
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.662, 64.374, 70.468
Angle α, β, γ (deg.)90.00, 96.33, 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: 29968.098 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 514-769
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06401
#2: Chemical ChemComp-OR8 / 2-CHLORO-N-[[4-(3,5-DIMETHYLISOXAZOL-4-YL)PHENYL]METHYL]-1,4-DIMETHYL-1H-PYRAZOLE-4-SULFONAMIDE


Mass: 394.876 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19ClN4O3S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-A2K / (8S,11R,13S,14S,16S,17S)-17-cyclopropylcarbonyl-16-ethenyl-13-methyl-11-(4-pyridin-3-ylphenyl)-2,6,7,8,11,12,14,15,16,17-decahydro-1H-cyclopenta[a]phenanthren-3-one


Mass: 503.674 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H37NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growpH: 6.5
Details: 20-30% POLYETHYLENE GLYCOL 3350, 0.1 M HEPES PH 6.5, 100 MM MG2SO4, 10% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: R-AXIS / Detector: IMAGE PLATE / Date: Mar 10, 2011 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→47.4 Å / Num. obs: 40585 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 4 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
d*TREKdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3ZR7

3zr7


Resolution: 1.9→70.04 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 12.436 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2516 2126 5.2 %RANDOM
Rwork0.20549 ---
obs0.20788 38443 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.637 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å20.53 Å2
2---0.69 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.9→70.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4043 0 69 161 4273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.024209
X-RAY DIFFRACTIONr_bond_other_d0.0010.022883
X-RAY DIFFRACTIONr_angle_refined_deg1.4762.0035706
X-RAY DIFFRACTIONr_angle_other_deg0.94637074
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5075498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4924.368174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57115788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5271520
X-RAY DIFFRACTIONr_chiral_restr0.0680.2655
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214495
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02821
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 146 -
Rwork0.401 2760 -
obs--99.76 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2918-0.27450.10052.46020.09611.4952-0.0502-0.0681-0.07350.11680.0080.07740.1639-0.08970.04220.1360.00040.0260.0140.01470.0672-7.38612.4911.76
21.61120.1172-0.99771.90160.50672.41960.0894-0.14180.10420.0458-0.0321-0.0195-0.03440.2859-0.05730.0526-0.0086-0.04560.1168-0.0110.065813.3030.44236.869
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A683 - 931
2X-RAY DIFFRACTION1A1933 - 1934
3X-RAY DIFFRACTION2B683 - 932
4X-RAY DIFFRACTION2B1933

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