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Yorodumi- PDB-4iqr: Multi-Domain Organization of the HNF4alpha Nuclear Receptor Compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4iqr | ||||||
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Title | Multi-Domain Organization of the HNF4alpha Nuclear Receptor Complex on DNA | ||||||
Components |
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Keywords | Transcription/DNA / Transcription Factor / Transcription-DNA complex | ||||||
Function / homology | Function and homology information regulation of growth hormone receptor signaling pathway / ornithine metabolic process / regulation of gastrulation / Nephron development / sex differentiation / phospholipid homeostasis / signal transduction involved in regulation of gene expression / triglyceride homeostasis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / lipid homeostasis ...regulation of growth hormone receptor signaling pathway / ornithine metabolic process / regulation of gastrulation / Nephron development / sex differentiation / phospholipid homeostasis / signal transduction involved in regulation of gene expression / triglyceride homeostasis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / lipid homeostasis / locomotor rhythm / Regulation of gene expression in beta cells / regulation of insulin secretion / 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 / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / response to glucose / 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 / xenobiotic metabolic process / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / response to progesterone / cholesterol homeostasis / fatty acid binding / nuclear receptor binding / circadian regulation of gene expression / Heme signaling / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / lipid metabolic process / PPARA activates gene expression / Cytoprotection by HMOX1 / negative regulation of cell growth / 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 / blood coagulation / rhythmic process / Circadian Clock / glucose homeostasis / HATs acetylate histones / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / transcription by RNA polymerase II / transcription coactivator activity / cell differentiation / 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 / negative regulation of cell population proliferation / signaling receptor binding / negative regulation of DNA-templated transcription / 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 / protein homodimerization activity / 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: 2.9 Å | ||||||
Authors | Chandra, V. / Huang, P. / Kim, Y. / Rastinejad, F. | ||||||
Citation | Journal: Nature / Year: 2013 Title: Multidomain integration in the structure of the HNF-4 alpha nuclear receptor complex. Authors: Chandra, V. / Huang, P. / Potluri, N. / Wu, D. / Kim, Y. / Rastinejad, F. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4iqr.cif.gz | 305.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4iqr.ent.gz | 241.4 KB | Display | PDB format |
PDBx/mmJSON format | 4iqr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4iqr_validation.pdf.gz | 546.9 KB | Display | wwPDB validaton report |
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Full document | 4iqr_full_validation.pdf.gz | 595.2 KB | Display | |
Data in XML | 4iqr_validation.xml.gz | 51.6 KB | Display | |
Data in CIF | 4iqr_validation.cif.gz | 68.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/4iqr ftp://data.pdbj.org/pub/pdb/validation_reports/iq/4iqr | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-DNA chain , 2 types, 4 molecules CGDH
#2: DNA chain | Mass: 6232.056 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: DNA chain | Mass: 6035.902 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Protein / Protein/peptide , 2 types, 8 molecules ABEFIJKL
#1: Protein | Mass: 38567.598 Da / Num. of mol.: 4 / Fragment: unp residues 55-377 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HNF4A, HNF4, NR2A1, TCF14 / Production host: Escherichia coli (E. coli) / References: UniProt: P41235 #4: Protein/peptide | Mass: 1621.902 Da / Num. of mol.: 4 / Fragment: LxxLL motif peptide (unp residues 685-697) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596 |
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-Non-polymers , 2 types, 12 molecules
#5: Chemical | ChemComp-MYR / #6: Chemical | ChemComp-ZN / |
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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: 3.08 Å3/Da / Density % sol: 60.03 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES, 25mM NH4Cl, 25mM MgCl2 and PEG 3350 , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 14, 2011 |
Radiation | Monochromator: Rosenbaum-Rock high-resolution double-crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. all: 51050 / Num. obs: 50948 / % possible obs: 99.8 % / Redundancy: 4.1 % / Rsym value: 0.083 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2 / Rsym value: 0.688 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entries 3FS1 and 3CBB Resolution: 2.9→48.81 Å / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 87.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→48.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.019
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