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- PDB-3zra: Structural basis for agonism and antagonism for a set of chemical... -

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Entry
Database: PDB / ID: 3zra
TitleStructural basis for agonism and antagonism for a set of chemically related progesterone receptor modulators
ComponentsPROGESTERONE RECEPTOR
KeywordsHORMONE RECEPTOR
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-ORB / Progesterone receptor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.9 Å
AuthorsLusher, S.J. / Raaijmakers, H.C.A. / Vu-Pham, D. / Dechering, K. / Wai Lam, T. / Brown, A.R. / Hamilton, N.M. / Nimz, O. / Azevedo, R. / McGuire, R. ...Lusher, S.J. / Raaijmakers, H.C.A. / Vu-Pham, D. / Dechering, K. / Wai Lam, T. / Brown, A.R. / Hamilton, N.M. / Nimz, O. / Azevedo, R. / McGuire, R. / Oubrie, A. / de Vlieg, J.
CitationJournal: J. Biol. Chem. / Year: 2011
Title: Structural basis for agonism and antagonism for a set of chemically related progesterone receptor modulators.
Authors: Lusher, S.J. / Raaijmakers, H.C. / Vu-Pham, D. / Dechering, K. / Lam, T.W. / Brown, A.R. / Hamilton, N.M. / Nimz, O. / Bosch, R. / McGuire, R. / Oubrie, A. / de Vlieg, J.
History
DepositionJun 15, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Dec 27, 2017Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name

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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)60,8525
Polymers59,9362
Non-polymers9163
Water1,53185
1
A: PROGESTERONE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4743
Polymers29,9681
Non-polymers5062
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROGESTERONE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3782
Polymers29,9681
Non-polymers4101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.305, 64.114, 69.932
Angle α, β, γ (deg.)90.00, 96.53, 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 678-933
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-ORB / N-{(1R)-1-[4-(2-CHLORO-5-FLUOROPYRIDIN-3-YL)PHENYL]ETHYL}-3,5-DIMETHYLISOXAZOLE-4-SULFONAMIDE


Mass: 409.862 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H17ClFN3O3S
#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.: 85 / 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: 2.18 Å3/Da / Density % sol: 43 % / Description: NONE
Crystal growpH: 6.5
Details: 20-30% POLYETHYLENE GLYCOL 3350, 0.1M HEPES PH 6.5, 100 MM MG2SO4, 10% GLYCEROL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 16, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.9→28.11 Å / Num. obs: 38129 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.3
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 2.6 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
CrystalCleardata reduction
DTSCALEAVERAGEdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.9→28.12 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 9.732 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24844 1963 5.1 %RANDOM
Rwork0.21164 ---
obs0.21357 36165 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: 37.03 Å2
Baniso -1Baniso -2Baniso -3
1-2.43 Å20 Å21.19 Å2
2---1.09 Å20 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4048 0 59 85 4192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224213
X-RAY DIFFRACTIONr_bond_other_d0.0010.022872
X-RAY DIFFRACTIONr_angle_refined_deg1.1281.9975708
X-RAY DIFFRACTIONr_angle_other_deg0.83637043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9555500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.33224.343175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75115791
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0281520
X-RAY DIFFRACTIONr_chiral_restr0.0610.2649
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214506
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02815
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_it0.531.52506
X-RAY DIFFRACTIONr_mcbond_other0.1251.5998
X-RAY DIFFRACTIONr_mcangle_it0.98724074
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.60631707
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5724.51634
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
Rfree0.348 150 -
Rwork0.31 2598 -
obs--100 %
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)
11.28630.5746-0.66291.54960.58092.49850.1326-0.16850.17170.13880.01450.09-0.06870.4656-0.14710.1799-0.00740.01560.2182-0.01310.034716.8060.0291.747
21.0533-0.39470.10262.1418-0.14941.3626-0.0407-0.0376-0.10290.11970.04590.07840.0194-0.0829-0.00520.08950.00560.00820.02090.00910.0137-3.52112.148-33.033
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A683 - 932
2X-RAY DIFFRACTION2B683 - 932

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