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- PDB-1e3k: Human Progesteron Receptor Ligand Binding Domain in complex with ... -

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Basic information

Entry
Database: PDB / ID: 1e3k
TitleHuman Progesteron Receptor Ligand Binding Domain in complex with the ligand metribolone (R1881)
ComponentsPROGESTERONE RECEPTOR
KeywordsHUMAN PROGESTERONE RECEPTOR / LIGAND BINDING DOMAIN
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-R18 / Progesterone receptor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMatias, P.M. / Donner, P. / Coelho, R. / Thomaz, M. / Peixoto, C. / Macedo, S. / Otto, N. / Joschko, S. / Scholz, P. / Wegg, A. ...Matias, P.M. / Donner, P. / Coelho, R. / Thomaz, M. / Peixoto, C. / Macedo, S. / Otto, N. / Joschko, S. / Scholz, P. / Wegg, A. / Basler, S. / Schafer, M. / Egner, U. / Carrondo, M.A.
CitationJournal: J. Biol. Chem. / Year: 2000
Title: Structural evidence for ligand specificity in the binding domain of the human androgen receptor. Implications for pathogenic gene mutations.
Authors: Matias, P.M. / Donner, P. / Coelho, R. / Thomaz, M. / Peixoto, C. / Macedo, S. / Otto, N. / Joschko, S. / Scholz, P. / Wegg, A. / Basler, S. / Schafer, M. / Egner, U. / Carrondo, M.A.
History
DepositionJun 19, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Structure summary
Category: citation / entity_src_gen / struct
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _struct.title
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)60,0464
Polymers59,4782
Non-polymers5692
Water181
1
A: PROGESTERONE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0232
Polymers29,7391
Non-polymers2841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PROGESTERONE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0232
Polymers29,7391
Non-polymers2841
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)58.402, 65.011, 71.181
Angle α, β, γ (deg.)90.00, 95.65, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.52983, 0.82973, 0.17561), (0.83611, -0.54571, 0.05579), (0.14212, 0.11726, -0.98288)
Vector: 3.26396, -13.18369, 32.57034)

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Components

#1: Protein PROGESTERONE RECEPTOR /


Mass: 29738.824 Da / Num. of mol.: 2 / Fragment: LIGAND-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P06401
#2: Chemical ChemComp-R18 / (17BETA)-17-HYDROXY-17-METHYLESTRA-4,9,11-TRIEN-3-ONE / METHYLTRIENOLONE / 17BETA-HYDROXY-17METHYL-19NORANDROSTA-4,9,11-TRIEN-3-ONE / R1881 / Metribolone


Mass: 284.393 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H24O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: RESERVOIR SOLUTION: 10% ISO-PROPANOL, 100MM SODIUM CITRATE 50MM HEPES PH 7.5. THE DROPS WERE SET UP USING THE HANGING DROP METHOD AND WERE COMPOSED OF A 2:1 RATIO OF PROTEIN AND RESERVOIR SOLUTIONS.
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13 mg/mlprotein1drop
210 %isopropyl alcohol1reservoir
3100 mMsodium citrate1reservoir
450 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9537
DetectorType: MARRESEARCH / Detector: CCD / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.8→12.5 Å / Num. obs: 8875 / % possible obs: 67 % / Redundancy: 7.6 % / Biso Wilson estimate: 48.2 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 15.2
Reflection shellResolution: 2.8→2.87 Å / Rmerge(I) obs: 0.151 / % possible all: 68.8
Reflection
*PLUS
Num. measured all: 67655
Reflection shell
*PLUS
% possible obs: 68.8 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A28

1a28


Resolution: 2.8→12.5 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: FINAL 2 C-TERMINAL RESIDUES NOT SEEN IN THE MAP
RfactorNum. reflection% reflectionSelection details
Rfree0.343 -5 %RANDOM
Rwork0.217 ---
obs0.24 8875 67 %-
Refinement stepCycle: LAST / Resolution: 2.8→12.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4027 0 42 1 4070
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.044
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS

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