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Yorodumi- PDB-7tt8: Human LRH-1 LBD bound to agonist 6N-10CA and fragment of Tif2 coa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tt8 | ||||||||||||||||||
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Title | Human LRH-1 LBD bound to agonist 6N-10CA and fragment of Tif2 coactivator | ||||||||||||||||||
Components |
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Keywords | NUCLEAR PROTEIN / LRH-1 / Nuclear Receptor / Ligand / Synthetic Agonist | ||||||||||||||||||
Function / homology | Function and homology information Regulation of gene expression in early pancreatic precursor cells / pancreas morphogenesis / calcineurin-mediated signaling / acinar cell differentiation / tissue development / bile acid metabolic process / embryo development ending in birth or egg hatching / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / homeostatic process / locomotor rhythm ...Regulation of gene expression in early pancreatic precursor cells / pancreas morphogenesis / calcineurin-mediated signaling / acinar cell differentiation / tissue development / bile acid metabolic process / embryo development ending in birth or egg hatching / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / homeostatic process / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / positive regulation of viral genome replication / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Recycling of bile acids and salts / cellular response to hormone stimulus / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / regulation of cellular response to insulin stimulus / hormone-mediated signaling pathway / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / cellular response to leukemia inhibitory factor / transcription coregulator binding / response to progesterone / cholesterol homeostasis / nuclear receptor binding / circadian regulation of gene expression / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / phospholipid binding / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / Circadian Clock / regulation of cell population proliferation / HATs acetylate histones / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / sequence-specific DNA binding / transcription coactivator activity / nuclear body / protein dimerization activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||||||||||||||
Authors | Cato, M.L. / Ortlund, E.A. | ||||||||||||||||||
Funding support | United States, 5items
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Citation | Journal: J.Med.Chem. / Year: 2022 Title: Differential Modulation of Nuclear Receptor LRH-1 through Targeting Buried and Surface Regions of the Binding Pocket. Authors: Cato, M.L. / Cornelison, J.L. / Spurlin, R.M. / Courouble, V.V. / Patel, A.B. / Flynn, A.R. / Johnson, A.M. / Okafor, C.D. / Frank, F. / D'Agostino, E.H. / Griffin, P.R. / Jui, N.T. / Ortlund, E.A. #1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010 Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution. Authors: Adams, P.D. / Afonine, P.V. / Bunkoczi, G. / Chen, V.B. / Davis, I.W. / Echols, N. / Headd, J.J. / Hung, L.W. / Kapral, G.J. / Grosse-Kunstleve, R.W. / McCoy, A.J. / Moriarty, N.W. / ...Authors: Adams, P.D. / Afonine, P.V. / Bunkoczi, G. / Chen, V.B. / Davis, I.W. / Echols, N. / Headd, J.J. / Hung, L.W. / Kapral, G.J. / Grosse-Kunstleve, R.W. / McCoy, A.J. / Moriarty, N.W. / Oeffner, R. / Read, R.J. / Richardson, D.C. / Richardson, J.S. / Terwilliger, T.C. / Zwart, P.H. #2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010 Title: Features and development of Coot. Authors: Emsley, P. / Lohkamp, B. / Scott, W.G. / Cowtan, K. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tt8.cif.gz | 195 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tt8.ent.gz | 130.7 KB | Display | PDB format |
PDBx/mmJSON format | 7tt8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tt8_validation.pdf.gz | 761.7 KB | Display | wwPDB validaton report |
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Full document | 7tt8_full_validation.pdf.gz | 764.3 KB | Display | |
Data in XML | 7tt8_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 7tt8_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/7tt8 ftp://data.pdbj.org/pub/pdb/validation_reports/tt/7tt8 | HTTPS FTP |
-Related structure data
Related structure data | 5l11S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28401.771 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NR5A2, B1F, CPF, FTF / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O00482 |
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#2: Protein/peptide | Mass: 1708.931 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596 |
#3: Chemical | ChemComp-IUW / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.19 Å3/Da / Density % sol: 70.66 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: tri-Na citrate (4.6), tert-butanol, glycerol |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→35.2 Å / Num. obs: 11868 / % possible obs: 97.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 45.17 Å2 / CC1/2: 0.978 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.8→2.9 Å / Num. unique obs: 1181 / CC1/2: 0.72 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5L11 Resolution: 2.8→35.2 Å / SU ML: 0.3541 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 28.4437 / Stereochemistry target values: CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→35.2 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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