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Yorodumi- PDB-4qjr: Crystal structure of human nuclear receptor sf-1 (nr5a1) bound to... -
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-Basic information
Entry | Database: PDB / ID: 4qjr | ||||||
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Title | Crystal structure of human nuclear receptor sf-1 (nr5a1) bound to its hormone pip3 at 2.4 a resolution | ||||||
Components |
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Keywords | TRANSCRIPTION FACTOR/HORMONE / NUCLEAR HORMONE RECEPTOR / NR5A1 / SF-1 LIGAND BINDINGNUCLEAR DOMAIN / REGULATORY LIGANDS / TRANSCRIPTION / TRANSCRIPTION REGULATION / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY / PARTNERSHIP FOR STEM CELL BIOLOGY / PIP3 / PIP2 / NUCLEUS / NUCLEAR PHOSPHATIDYLINOSITOL PHOSPHATES / TRANSCRIPTION FACTOR-HORMONE complex / STEMCELL | ||||||
Function / homology | Function and homology information primary sex determination / Sertoli cell differentiation / negative regulation of female gonad development / Regulation of MITF-M dependent genes involved in metabolism / sex determination / positive regulation of male gonad development / regulation of steroid biosynthetic process / luteinization / Transcriptional regulation of testis differentiation / Transcriptional regulation of pluripotent stem cells ...primary sex determination / Sertoli cell differentiation / negative regulation of female gonad development / Regulation of MITF-M dependent genes involved in metabolism / sex determination / positive regulation of male gonad development / regulation of steroid biosynthetic process / luteinization / Transcriptional regulation of testis differentiation / Transcriptional regulation of pluripotent stem cells / tissue development / positive regulation of fatty acid oxidation / Leydig cell differentiation / male sex determination / maintenance of protein location in nucleus / hormone metabolic process / response to muscle activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / cellular respiration / lncRNA binding / digestion / adrenal gland development / temperature homeostasis / female gonad development / response to starvation / intracellular glucose homeostasis / fatty acid oxidation / response to dietary excess / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / hormone-mediated signaling pathway / adipose tissue development / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / brown fat cell differentiation / energy homeostasis / transcription coregulator activity / positive regulation of gluconeogenesis / transcription coregulator binding / respiratory electron transport chain / RNA splicing / negative regulation of smooth muscle cell proliferation / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / mitochondrion organization / SUMOylation of intracellular receptors / gluconeogenesis / nuclear receptor binding / regulation of circadian rhythm / transcription initiation at RNA polymerase II promoter / RNA polymerase II transcription regulatory region sequence-specific DNA binding / PPARA activates gene expression / positive regulation of DNA-binding transcription factor activity / circadian regulation of gene expression / Heme signaling / Nuclear Receptor transcription pathway / Transcriptional activation of mitochondrial biogenesis / Transcriptional regulation of white adipocyte differentiation / PML body / chromatin DNA binding / RNA polymerase II transcription regulator complex / phospholipid binding / nuclear receptor activity / mRNA processing / Regulation of RUNX2 expression and activity / male gonad development / sequence-specific double-stranded DNA binding / Circadian Clock / positive regulation of cold-induced thermogenesis / cellular response to oxidative stress / DNA-binding transcription factor binding / protein-containing complex assembly / neuron apoptotic process / sequence-specific DNA binding / transcription coactivator activity / negative regulation of neuron apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / protein stabilization / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / positive regulation of gene expression / positive regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) / Partnership for Stem Cell Biology (STEMCELL) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: The signaling phospholipid PIP3 creates a new interaction surface on the nuclear receptor SF-1. Authors: Blind, R.D. / Sablin, E.P. / Kuchenbecker, K.M. / Chiu, H.J. / Deacon, A.M. / Das, D. / Fletterick, R.J. / Ingraham, H.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qjr.cif.gz | 128.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qjr.ent.gz | 100 KB | Display | PDB format |
PDBx/mmJSON format | 4qjr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qjr_validation.pdf.gz | 775.6 KB | Display | wwPDB validaton report |
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Full document | 4qjr_full_validation.pdf.gz | 778.9 KB | Display | |
Data in XML | 4qjr_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 4qjr_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/4qjr ftp://data.pdbj.org/pub/pdb/validation_reports/qj/4qjr | HTTPS FTP |
-Related structure data
Related structure data | 4qk4C 1yowS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 27903.406 Da / Num. of mol.: 1 / Fragment: UNP residues 218-461 / Mutation: C247S, C412S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AD4BP, FTZF1, NR5A1, RC2003B, SF1 / Plasmid: pBH4 / Production host: Escherichia Coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13285 | ||||
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#2: Protein/peptide | Mass: 1523.854 Da / Num. of mol.: 1 / Fragment: UNP residues 139-152 / Source method: obtained synthetically Details: PGC-1ALPHA (PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA CO-ACTIVATOR-1ALPHA) PEPTIDE CONTAINING RESIDUES 139-EEPSLLKKLLLAPA-152 Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UBK2 | ||||
#3: Chemical | ChemComp-PIZ / ( | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | SF-1 (UNIPROT Q13285, NR5A1_HUMAN, STF1_HUMAN) LIGAND BINDING DOMAIN (LBD) WAS EXPRESSED WITH AN N- ...SF-1 (UNIPROT Q13285, NR5A1_HUMAN, STF1_HUMAN) LIGAND BINDING DOMAIN (LBD) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATI | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.98 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 10% PEG 8K, 0.025M MGOAC, 30% GLYCEROL, 0.067MM PIP3, 0.80MM 14MER EEPSLLKKLLLAPA, NANODROP, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K |
-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 2, 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: 2.4→29.165 Å / Num. all: 16205 / Num. obs: 16205 / % possible obs: 99.6 % / Redundancy: 11.9 % / Rsym value: 0.043 / Net I/σ(I): 24.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 1YOW Resolution: 2.4→29.165 Å / Occupancy max: 1 / Occupancy min: 0.17 / SU ML: 0.24 / σ(F): 2.03 / Phase error: 26.82 / 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: 148.66 Å2 / Biso mean: 76.3499 Å2 / Biso min: 34.79 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→29.165 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: 6
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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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