+Open data
-Basic information
Entry | Database: PDB / ID: 1m7w | ||||||
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Title | HNF4a ligand binding domain with bound fatty acid | ||||||
Components | Hepatocyte nuclear factor 4-alpha | ||||||
Keywords | TRANSCRIPTION FACTOR | ||||||
Function / homology | Function and homology information establishment of tissue polarity / response to trichostatin A / stearic acid binding / ornithine metabolic process / long-chain fatty acyl-CoA binding / long-chain fatty acyl-CoA hydrolase activity / regulation of gastrulation / regulation of microvillus assembly / acyl-CoA metabolic process / negative regulation of tyrosine phosphorylation of STAT protein ...establishment of tissue polarity / response to trichostatin A / stearic acid binding / ornithine metabolic process / long-chain fatty acyl-CoA binding / long-chain fatty acyl-CoA hydrolase activity / regulation of gastrulation / regulation of microvillus assembly / acyl-CoA metabolic process / negative regulation of tyrosine phosphorylation of STAT protein / fatty-acyl-CoA binding / Nuclear Receptor transcription pathway / sex differentiation / positive regulation of fatty acid biosynthetic process / phospholipid homeostasis / signal transduction involved in regulation of gene expression / hepatocyte differentiation / cell-cell junction organization / triglyceride homeostasis / arachidonate binding / negative regulation of protein import into nucleus / response to dexamethasone / lipid homeostasis / regulation of lipid metabolic process / negative regulation of mitotic cell cycle / cis-regulatory region sequence-specific DNA binding / response to glucose / positive regulation of gluconeogenesis / response to cAMP / regulation of insulin secretion / xenobiotic metabolic process / transcription corepressor binding / response to nutrient levels / cholesterol homeostasis / negative regulation of cell migration / transcription coregulator binding / fatty acid binding / regulation of circadian rhythm / negative regulation of cell growth / lipid metabolic process / nuclear receptor activity / sequence-specific double-stranded DNA binding / blood coagulation / rhythmic process / glucose homeostasis / cellular response to hypoxia / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / response to lipopolysaccharide / transcription by RNA polymerase II / cell differentiation / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / response to xenobiotic stimulus / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / negative regulation of cell population proliferation / signaling receptor binding / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / protein-containing complex binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus rattus (black rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å | ||||||
Authors | Dhe-Paganon, S. / Duda, K. / Iwamoto, M. / Chi, Y.I. / Shoelson, S.E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Crystal structure of the HNF4 alpha ligand binding domain in complex with endogenous fatty acid ligand Authors: Dhe-Paganon, S. / Duda, K. / Iwamoto, M. / Chi, Y.I. / Shoelson, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m7w.cif.gz | 182.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m7w.ent.gz | 148.3 KB | Display | PDB format |
PDBx/mmJSON format | 1m7w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m7w_validation.pdf.gz | 408.6 KB | Display | wwPDB validaton report |
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Full document | 1m7w_full_validation.pdf.gz | 453.6 KB | Display | |
Data in XML | 1m7w_validation.xml.gz | 24.8 KB | Display | |
Data in CIF | 1m7w_validation.cif.gz | 35.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m7/1m7w ftp://data.pdbj.org/pub/pdb/validation_reports/m7/1m7w | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
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Unit cell |
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-Components
#1: Protein | Mass: 28120.455 Da / Num. of mol.: 4 / Fragment: Residues 133-382 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus rattus (black rat) / Gene: HNF4a / Plasmid: pet28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P22449 #2: Chemical | ChemComp-DAO / #3: Water | ChemComp-HOH / | |
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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: 2.65 Å3/Da / Density % sol: 53.52 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C |
Detector | Type: BRANDEIS - B1.2 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. obs: 29727 / Observed criterion σ(I): 0.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.8→20 Å /
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refinement | *PLUS Rfactor Rwork: 0.232 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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