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- PDB-1yok: crystal structure of human LRH-1 bound with TIF-2 peptide and pho... -
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Basic information
Entry | Database: PDB / ID: 1yok | ||||||
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Title | crystal structure of human LRH-1 bound with TIF-2 peptide and phosphatidylglycerol | ||||||
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![]() | TRANSCRIPTION / LRH-1 / TIF-1 / phosphatidylglycerol | ||||||
Function / homology | ![]() 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 / regulation of cellular response to insulin stimulus / 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 / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Krylova, I.N. / Sablin, E.P. / Moore, J. / Xu, R.X. / Waitt, G.M. / MacKay, J.A. / Juzumiene, D. / Bynum, J.M. / Madauss, K. / Montana, V. ...Krylova, I.N. / Sablin, E.P. / Moore, J. / Xu, R.X. / Waitt, G.M. / MacKay, J.A. / Juzumiene, D. / Bynum, J.M. / Madauss, K. / Montana, V. / Lebedeva, L. / Suzawa, M. / Williams, J.D. / Williams, S.P. / Guy, R.K. / Thornton, J.W. / Fletterick, R.J. / Willson, T.M. / Ingraham, H.A. | ||||||
![]() | ![]() Title: Structural analyses reveal phosphatidyl inositols as ligands for the NR5 orphan receptors SF-1 and LRH-1. Authors: Krylova, I.N. / Sablin, E.P. / Moore, J. / Xu, R.X. / Waitt, G.M. / MacKay, J.A. / Juzumiene, D. / Bynum, J.M. / Madauss, K. / Montana, V. / Lebedeva, L. / Suzawa, M. / Williams, J.D. / ...Authors: Krylova, I.N. / Sablin, E.P. / Moore, J. / Xu, R.X. / Waitt, G.M. / MacKay, J.A. / Juzumiene, D. / Bynum, J.M. / Madauss, K. / Montana, V. / Lebedeva, L. / Suzawa, M. / Williams, J.D. / Williams, S.P. / Guy, R.K. / Thornton, J.W. / Fletterick, R.J. / Willson, T.M. / Ingraham, H.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.2 KB | Display | ![]() |
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PDB format | ![]() | 50.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 700.2 KB | Display | ![]() |
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Full document | ![]() | 712.3 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 19.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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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Components
#1: Protein | Mass: 29800.523 Da / Num. of mol.: 1 Fragment: sequence database residues 300-541: contains ligand binding domain (residues 346-388) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Protein/peptide | Mass: 1708.931 Da / Num. of mol.: 2 / Fragment: sequence database residues 740-753 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human). References: UniProt: Q15596 #3: Chemical | ChemComp-P6L / ( | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 10 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.9 Details: Sodium potassium phosphate, glycerol, ethylene glycol, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 15, 2003 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 11732 / Num. obs: 11298 / % possible obs: 95.6 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 2.5 / Redundancy: 6.7 % / Biso Wilson estimate: 56 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 44 |
Reflection shell | Resolution: 2.5→2.58 Å / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.5 / Num. unique all: 829 / Rsym value: 0.42 / % possible all: 72.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Human SF-1 Resolution: 2.5→40 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→40 Å
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Refine LS restraints |
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