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- PDB-1qkm: HUMAN OESTROGEN RECEPTOR BETA LIGAND-BINDING DOMAIN IN COMPLEX WI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1qkm | ||||||
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Title | HUMAN OESTROGEN RECEPTOR BETA LIGAND-BINDING DOMAIN IN COMPLEX WITH PARTIAL AGONIST GENISTEIN | ||||||
![]() | ESTROGEN RECEPTOR BETA | ||||||
![]() | NUCLEAR RECEPTOR / TRANSCRIPTION FACTOR / PHYTO-OESTROGEN / PARTIAL AGONIST | ||||||
Function / homology | ![]() receptor antagonist activity / nuclear steroid receptor activity / nuclear estrogen receptor activity / estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / steroid binding / ESR-mediated signaling / cellular response to estradiol stimulus / negative regulation of cell growth ...receptor antagonist activity / nuclear steroid receptor activity / nuclear estrogen receptor activity / estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / steroid binding / ESR-mediated signaling / cellular response to estradiol stimulus / negative regulation of cell growth / positive regulation of DNA-binding transcription factor activity / Nuclear Receptor transcription pathway / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / PIP3 activates AKT signaling / cell-cell signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Extra-nuclear estrogen signaling / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pike, A.C.W. / Brzozowski, A.M. / Carlquist, M. | ||||||
![]() | ![]() Title: Structure of the Ligand-Binding Domain of Oestrogen Receptor Beta in the Presence of a Partial Agonist and a Full Antagonist Authors: Pike, A.C.W. / Brzozowski, A.M. / Hubbard, R.E. / Bonn, T. / Thorsell, A.-G. / Engstrom, O. / Ljunggren, J. / Gustaffson, J.-A. / Carlquist, M. #1: ![]() Title: Molecular Basis of Agonism and Antagonism in the Oestrogen Receptor Authors: Brzozowski, A.M. / Pike, A.C.W. / Dauter, Z. / Hubbard, R.E. / Bonn, T. / Engstrom, O. / Ohman, L. / Greene, G.L. / Gustaffson, J.-A. / Carlquist, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64 KB | Display | ![]() |
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PDB format | ![]() | 46.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 686.7 KB | Display | ![]() |
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Full document | ![]() | 689.9 KB | Display | |
Data in XML | ![]() | 12.6 KB | Display | |
Data in CIF | ![]() | 17.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qknC ![]() 1ereS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | BIOLOGICAL_UNIT: DIMER |
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Components
#1: Protein | Mass: 28726.092 Da / Num. of mol.: 1 / Fragment: LIGAND-BINDING DOMAIN Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH THE PHYTO-OESTROGEN GENISTEIN / Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-GEN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.1 Details: 6-9% (W/V) PEG 6000, 1.6-2.1M NACL, 0.1M TRIS-HCL, PH 8.1 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: drop consists of equal volume of protein and reservoir solutions | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→60 Å / Num. obs: 28523 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 8 % / Biso Wilson estimate: 32.6 Å2 / Rsym value: 0.049 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 8 % / Mean I/σ(I) obs: 4 / Rsym value: 0.433 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 358818 / Rmerge(I) obs: 0.049 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.433 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ERE Resolution: 1.8→55 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12715 / ESU R Free: 0.12556 Details: BULK SOLVENT CORRECTION CALCULATED IN XPLOR V3.843 WAS USED THROUGHOUT. DISCREPANCY BETWEEN REFINEMENT STATISTICS GIVEN ABOVE AND PUBLISHED VALUES ARISE DUE TO A SEQUENCE ERROR THAT HAS ...Details: BULK SOLVENT CORRECTION CALCULATED IN XPLOR V3.843 WAS USED THROUGHOUT. DISCREPANCY BETWEEN REFINEMENT STATISTICS GIVEN ABOVE AND PUBLISHED VALUES ARISE DUE TO A SEQUENCE ERROR THAT HAS SUBSEQUENTLY BEEN CORRECTED.
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Displacement parameters | Biso mean: 41.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→55 Å
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Refine LS restraints |
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