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- PDB-1a28: HORMONE-BOUND HUMAN PROGESTERONE RECEPTOR LIGAND-BINDING DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1a28
TitleHORMONE-BOUND HUMAN PROGESTERONE RECEPTOR LIGAND-BINDING DOMAIN
ComponentsPROGESTERONE RECEPTOR
KeywordsPROGESTERONE RECEPTOR / STEROID RECEPTOR / NUCLEAR RECEPTOR / TRANSCRIPTION REGULATION
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 / intracellular steroid hormone receptor signaling pathway ...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 / intracellular steroid hormone receptor 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 / 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
PROGESTERONE / Progesterone receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, MIR / Resolution: 1.8 Å
AuthorsSigler, P.B. / Williams, S.P.
CitationJournal: Nature / Year: 1998
Title: Atomic structure of progesterone complexed with its receptor.
Authors: Williams, S.P. / Sigler, P.B.
History
DepositionJan 19, 1998Processing site: BNL
Revision 1.0Jul 15, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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)59,7384
Polymers59,1092
Non-polymers6292
Water3,243180
1
A: PROGESTERONE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8692
Polymers29,5551
Non-polymers3141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROGESTERONE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8692
Polymers29,5551
Non-polymers3141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.123, 64.444, 69.954
Angle α, β, γ (deg.)90.00, 95.74, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.536461, -0.825673, 0.174566), (-0.8309, -0.552959, -0.061968), (0.147693, -0.111803, -0.982694)
Vector: 23.282, 62.039, 100.634)

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Components

#1: Protein PROGESTERONE RECEPTOR /


Mass: 29554.633 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: BREAST CANCER / Cell line: T47-D / Gene: PGR / Plasmid: PPR677-933 / Species (production host): Escherichia coli / Gene (production host): PGR / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P06401
#2: Chemical ChemComp-STR / PROGESTERONE / Progesterone


Mass: 314.462 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30O2 / Comment: hormone*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.29 Å3/Da / Density % sol: 45.7 %
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLIZED FROM 2% PEG 4000, 50 MM PIPES PH 6.5, 350 MM LI2SO4, THEN STABILIZED IN THE SAME BUFFER WITH 21% ETHYLENE GLYCOL
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16.7 mMHEPES1drop
210 %glycerol1drop
33.3 mMdithiothreitol1drop
40.06 %beta-octylglucoside1drop
56.7 nMprogesterone1drop
693 mM1dropNaCl
74 mg/mlprotein1drop
817 mMPIPES1drop
9117 mM1dropLi2SO4
100.7 %PEG40001drop
1150 mMPIPES1reservoir
12350 mM1reservoirLi2SO4
132 %PEG40001reservoir
1410 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 12, 1997 / Details: SILICON CRYSTAL
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 42976 / % possible obs: 93.2 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.076 / Net I/σ(I): 18.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.055 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.319 / % possible all: 95.9

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Processing

Software
NameVersionClassification
DPHASEmodel building
CNS0.1refinement
DENZOdata reduction
SCALEPACKdata scaling
DPHASEphasing
RefinementMethod to determine structure: MAD, MIR / Resolution: 1.8→40 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.227 4081 8.5 %RANDOM
Rwork0.1905 ---
obs0.1905 40453 84.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.73 Å2 / ksol: 0.377 e/Å3
Displacement parametersBiso mean: 32.8 Å2
Baniso -1Baniso -2Baniso -3
1--5.368 Å20 Å2-3.239 Å2
2---0.11 Å20 Å2
3---5.478 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4036 0 46 180 4262
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.392
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.18
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.904
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.9021.5
X-RAY DIFFRACTIONc_mcangle_it3.2861
X-RAY DIFFRACTIONc_scbond_it4.9122
X-RAY DIFFRACTIONc_scangle_it6.2081.4
LS refinement shellResolution: 1.8→1.86 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.252 335 11.2 %
Rwork0.208 2998 -
obs--70.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PROG_CSD.PARPROG_CSD.TOP
Software
*PLUS
Name: CNS / Version: 0.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.2279
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008343
X-RAY DIFFRACTIONc_angle_deg1.3928
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.18444
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.90455
LS refinement shell
*PLUS
Rfactor Rfree: 0.252 / Rfactor Rwork: 0.208

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