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- PDB-3d90: Crystal structure of the human progesterone receptor ligand-bindi... -

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Basic information

Entry
Database: PDB / ID: 3d90
TitleCrystal structure of the human progesterone receptor ligand-binding domain bound to levonorgestrel
ComponentsProgesterone receptor
KeywordsTRANSCRIPTION / progesterone receptor / steroid receptor / nuclear receptor / transcription factor / women health / contraception / Alternative splicing / DNA-binding / Lipid-binding / Metal-binding / Nucleus / Phosphoprotein / Polymorphism / Receptor / Steroid-binding / Transcription regulation / 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 / Nuclear signaling by ERBB4 ...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 / Nuclear signaling by ERBB4 / intracellular steroid hormone receptor signaling pathway / 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-NOG / Progesterone receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsPetit-Topin, I. / Turque, N. / Ulman, A. / Gainer, E. / Rafestin-Oblin, M.E. / Fagart, J.
CitationJournal: Mol.Pharmacol. / Year: 2009
Title: Met909 plays a key role in the activation of the progesterone receptor and also in the high potency of 13-ethyl progestins
Authors: Petit-Topin, I. / Turque, N. / Fagart, J. / Fay, M. / Ulmann, A. / Gainer, E. / Rafestin-Oblin, M.E.
History
DepositionMay 26, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,1034
Polymers59,4782
Non-polymers6252
Water6,341352
1
A: Progesterone receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0512
Polymers29,7391
Non-polymers3121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Progesterone receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0512
Polymers29,7391
Non-polymers3121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.870, 65.310, 70.620
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: 29738.824 Da / Num. of mol.: 2 / Fragment: Ligand-binding domain, UNP residues 676-933
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: UV20HL21-27 / Gene: PGR, NR3C3 / Plasmid: PGEXHPRLBD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CODON PLUS (DE3) RIL / References: UniProt: P06401
#2: Chemical ChemComp-NOG / 13-BETA-ETHYL-17-ALPHA-ETHYNYL-17-BETA-HYDROXYGON-4-EN-3-ONE / NORGESTREL / Norgestrel


Mass: 312.446 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28O2 / Comment: hormone*YM
#3: 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: 2.27 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 8% PEG3350, x300mM MgSO4, 10% Glycerol 10%, 50mM PIPES, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 78 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979738 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 11, 2006 / Details: mirror 1, double crystal, mirror 2
RadiationMonochromator: sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979738 Å / Relative weight: 1
ReflectionResolution: 2.26→47.83 Å / Num. all: 25142 / Num. obs: 20345 / % possible obs: 80.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.76 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.067 / Net I/σ(I): 11.11
Reflection shellResolution: 2.26→2.3 Å / Redundancy: 2 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2.33 / Num. unique all: 939 / Rsym value: 0.332 / % possible all: 73.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
Xnemodata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SQN

1sqn


Resolution: 2.26→47.83 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1591596.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1058 5.2 %RANDOM
Rwork0.231 ---
obs0.231 20345 80.9 %-
all-25142 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.6464 Å2 / ksol: 0.354893 e/Å3
Displacement parametersBiso mean: 44 Å2
Baniso -1Baniso -2Baniso -3
1-26.34 Å20 Å21.22 Å2
2---9.62 Å20 Å2
3----16.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.26→47.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3967 0 46 352 4365
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.051.5
X-RAY DIFFRACTIONc_mcangle_it1.772
X-RAY DIFFRACTIONc_scbond_it1.542
X-RAY DIFFRACTIONc_scangle_it2.232.5
LS refinement shellResolution: 2.26→2.3 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 1058 5.1 %
Rwork0.23 2864 -
obs-20345 80.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2levo.paramlevo.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.top

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