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Yorodumi- PDB-4rwv: Crystal structure of PIP3 bound human nuclear receptor LRH-1 (Liv... -
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-Basic information
Entry | Database: PDB / ID: 4rwv | ||||||
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Title | Crystal structure of PIP3 bound human nuclear receptor LRH-1 (Liver Receptor Homolog 1, NR5A2) in complex with a co-regulator DAX-1 (NR0B1) peptide at 1.86 A resolution | ||||||
Components | (Nuclear receptor ...) x 2 | ||||||
Keywords | TRANSCRIPTION / Ligand-binding domain of nuclear hormone receptor / PF00104 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / Partnership for Stem Cell Biology / STEMCELL | ||||||
Function / homology | Function and homology information nuclear receptor binding => GO:0016922 / DNA hairpin binding / Sertoli cell differentiation / negative regulation of steroid biosynthetic process / Regulation of gene expression in early pancreatic precursor cells / AF-2 domain binding / pancreas morphogenesis / gonad development / calcineurin-mediated signaling / pituitary gland development ...nuclear receptor binding => GO:0016922 / DNA hairpin binding / Sertoli cell differentiation / negative regulation of steroid biosynthetic process / Regulation of gene expression in early pancreatic precursor cells / AF-2 domain binding / pancreas morphogenesis / gonad development / calcineurin-mediated signaling / pituitary gland development / acinar cell differentiation / tissue development / chromatin => GO:0000785 / negative regulation of intracellular steroid hormone receptor signaling pathway / Leydig cell differentiation / male sex determination / bile acid metabolic process / embryo development ending in birth or egg hatching / hypothalamus development / adrenal gland development / homeostatic process / transcription factor binding / centriolar satellite / response to immobilization stress / positive regulation of viral genome replication / hormone-mediated signaling pathway / cholesterol homeostasis / cellular response to leukemia inhibitory factor / transcription coregulator binding / transcription initiation at RNA polymerase II promoter / : / phospholipid binding / SUMOylation of intracellular receptors / protein localization / negative regulation of DNA-binding transcription factor activity / Nuclear Receptor transcription pathway / transcription corepressor activity / RNA polymerase II transcription regulator complex / male gonad development / nuclear receptor activity / sequence-specific double-stranded DNA binding / regulation of cell population proliferation / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.859 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) / Partnership for Stem Cell Biology / Partnership for Stem Cell Biology (STEMCELL) | ||||||
Citation | Journal: To be published Title: Crystal structure of a Homo sapiens hepatocytic transcription factor hB1F-2 (B1F2) in complex with nuclear receptor subfamily 0 group B member 1 (NR0B1, residues 140-154) from human at 1.86 A resolution Authors: Joint Center for Structural Genomics (JCSG) / Partnership for Stem Cell Biology | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rwv.cif.gz | 136.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rwv.ent.gz | 104.1 KB | Display | PDB format |
PDBx/mmJSON format | 4rwv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/4rwv ftp://data.pdbj.org/pub/pdb/validation_reports/rw/4rwv | HTTPS FTP |
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-Related structure data
Related structure data | 1yokS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Nuclear receptor ... , 2 types, 2 molecules AB
#1: Protein | Mass: 28733.102 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN (UNP residues 294-551) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B1F, CPF, FTF, NR5A2, RC2754B.LRH_1 / Plasmid: pRSF-2 Ek/LIC ligation independent cloning / Production host: Escherichia Coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O00482 |
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#2: Protein/peptide | Mass: 1651.904 Da / Num. of mol.: 1 / Fragment: UNP residues 140-154 / Source method: obtained synthetically / Details: comes from screening buffer as a peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: F1D8P4, UniProt: P51843*PLUS |
-Non-polymers , 4 types, 233 molecules
#3: Chemical | ChemComp-PIZ / ( | ||||
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#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-TRS / | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | LRH-1 (UNIPROT O00482, LIVER RECEPTOR HOMOLOG 1, NUCLEAR RECEPTOR SUBFAMILY 5 GROUP A MEMBER 2, ...LRH-1 (UNIPROT O00482, LIVER RECEPTOR HOMOLOG 1, NUCLEAR RECEPTOR SUBFAMILY 5 GROUP A MEMBER 2, NR5A2_HUMAN) LIGAND BINDING DOMAIN (LBD) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATI |
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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: 2.61 Å3/Da / Density % sol: 52.94 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: LRH-1/PIP3, 20% PEG 4K, 0.2M NaOAc, 0.1M Tris (8.5), 0.036mM PIP3, 0.90mM 15-mer PRQGSILYSLLTSSK, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2013 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.86→29.463 Å / Num. obs: 25922 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 32.31 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 11.72 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1YOK Resolution: 1.859→29.463 Å / Occupancy max: 1 / Occupancy min: 0.22 / SU ML: 0.23 / σ(F): 1.14 / Phase error: 22.91 / Stereochemistry target values: ML
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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 max: 110.47 Å2 / Biso mean: 39.0131 Å2 / Biso min: 13.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.859→29.463 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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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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