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- PDB-2ovm: Progesterone Receptor with Bound Asoprisnil and a Peptide from th... -

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Basic information

Entry
Database: PDB / ID: 2ovm
TitleProgesterone Receptor with Bound Asoprisnil and a Peptide from the Co-Repressor NCoR
Components
  • NCoR
  • Progesterone receptor
KeywordsTRANSCRIPTION / Progesterone Receptor / PR / Nuclear Receptor / Steroid Receptor / Co-Repressor / Asoprisnil / NCoR
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-AS0 / Progesterone receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMadauss, K.P. / Deng, S.-J. / Short, S.A. / Stewart, E.L. / Williams, S.P.
CitationJournal: Mol.Endocrinol. / Year: 2007
Title: A structural and in vitro characterization of asoprisnil: a selective progesterone receptor modulator.
Authors: Madauss, K.P. / Grygielko, E.T. / Deng, S.J. / Sulpizio, A.C. / Stanley, T.B. / Wu, C. / Short, S.A. / Thompson, S.K. / Stewart, E.L. / Laping, N.J. / Williams, S.P. / Bray, J.D.
History
DepositionFeb 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 4, 2019Group: Data collection / Category: reflns
Item: _reflns.d_resolution_low / _reflns.observed_criterion_sigma_F ..._reflns.d_resolution_low / _reflns.observed_criterion_sigma_F / _reflns.observed_criterion_sigma_I / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rsym_value / _reflns.pdbx_netI_over_sigmaI / _reflns.pdbx_redundancy
Revision 1.5Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Progesterone receptor
B: NCoR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6543
Polymers32,2052
Non-polymers4501
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-15 kcal/mol
Surface area12530 Å2
MethodPISA
2
A: Progesterone receptor
B: NCoR
hetero molecules

A: Progesterone receptor
B: NCoR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3086
Polymers64,4094
Non-polymers8992
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area6450 Å2
ΔGint-37 kcal/mol
Surface area22740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.514, 87.514, 90.412
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Progesterone receptor / PR


Mass: 29554.633 Da / Num. of mol.: 1 / Fragment: Ligand Binding Domain (residues 678-933)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGR, NR3C3 / Plasmid: pHis GST / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06401
#2: Protein/peptide NCoR


Mass: 2649.997 Da / Num. of mol.: 1 / Fragment: residues 2251-2275 / Source method: obtained synthetically / Details: synthesized peptide
#3: Chemical ChemComp-AS0 / 4-[(11BETA,17BETA)-17-METHOXY-17-(METHOXYMETHYL)-3-OXOESTRA-4,9-DIEN-11-YL]BENZALDEHYDE OXIME


Mass: 449.582 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H35NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 3.1 Å3/Da / Density % sol: 60.35 %
Crystal growTemperature: 277 K / pH: 8
Details: 0.1M Tris, 0.15M NaCl, 10% glycerol, pH 8.0, spontaneous crystallization, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 24, 2004 / Details: Osmic Blue mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 12673 / Num. obs: 12366 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 25.5

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Processing

Software
NameVersionClassificationNB
AMoREphasing
CNSrefinement
PDB_EXTRACT2data extraction
MAR345345DTBdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PR LBD from 1A28 minus residues 930-933

1a28


Resolution: 2.6→20 Å / FOM work R set: 0.856 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Maximum Likelihood target
RfactorNum. reflection% reflectionSelection details
Rfree0.244 849 6.7 %random
Rwork0.219 ---
all0.22 12673 --
obs0.22 12366 97.6 %-
Displacement parametersBiso mean: 25.648 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.02 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å / Luzzati sigma a obs: 0.266 Å
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2033 0 33 59 2125
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.201
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.6-2.660.302500.259672722
2.66-2.720.332430.258710753
2.72-2.790.275500.252686736
2.79-2.860.275590.253700759
2.86-2.940.285570.246678735
2.94-3.040.266560.24733789
3.04-3.150.253500.218711761
3.15-3.270.235480.228722770
3.27-3.420.271510.218703754
3.42-3.60.223600.206734794
3.6-3.830.225470.217725772
3.83-4.120.174490.178721770
4.12-4.530.219750.184725800
4.53-5.170.203550.175739794
5.17-6.480.345520.287754806
6.48-200.224470.212804851
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 DIFFRACTION5aso.par

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