+Open data
-Basic information
Entry | Database: PDB / ID: 1a28 | ||||||
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Title | HORMONE-BOUND HUMAN PROGESTERONE RECEPTOR LIGAND-BINDING DOMAIN | ||||||
Components | PROGESTERONE RECEPTOR | ||||||
Keywords | PROGESTERONE 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 / paracrine signaling / ovulation from ovarian follicle / regulation of epithelial cell proliferation / maintenance of protein location in nucleus / 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 / paracrine signaling / ovulation from ovarian follicle / regulation of epithelial cell proliferation / maintenance of protein location in nucleus / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD, MIR / Resolution: 1.8 Å | ||||||
Authors | Sigler, P.B. / Williams, S.P. | ||||||
Citation | Journal: Nature / Year: 1998 Title: Atomic structure of progesterone complexed with its receptor. Authors: Williams, S.P. / Sigler, P.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a28.cif.gz | 114.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a28.ent.gz | 89.1 KB | Display | PDB format |
PDBx/mmJSON format | 1a28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a28_validation.pdf.gz | 961.6 KB | Display | wwPDB validaton report |
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Full document | 1a28_full_validation.pdf.gz | 973.2 KB | Display | |
Data in XML | 1a28_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 1a28_validation.cif.gz | 30.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/1a28 ftp://data.pdbj.org/pub/pdb/validation_reports/a2/1a28 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.536461, -0.825673, 0.174566), Vector: |
-Components
#1: Protein | 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 | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 45.7 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 12, 1997 / Details: SILICON CRYSTAL |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.73 Å2 / ksol: 0.377 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å / Total num. of bins used: 10
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Xplor file |
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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
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LS refinement shell | *PLUS Rfactor Rfree: 0.252 / Rfactor Rwork: 0.208 |