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Yorodumi- PDB-1lv2: Hepatocyte Nuclear Factor 4 is a Transcription Factor that Consti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lv2 | ||||||
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Title | Hepatocyte Nuclear Factor 4 is a Transcription Factor that Constitutively Binds Fatty Acids | ||||||
Components | Hepatocyte nuclear factor 4-gamma | ||||||
Keywords | TRANSCRIPTION / diabetes / fatty acids / HNF4 / MODY / nuclear receptor / transcription factor | ||||||
Function / homology | Function and homology information anatomical structure development / chromatin => GO:0000785 / Regulation of gene expression in beta cells / transcription initiation at RNA polymerase II promoter / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Nuclear Receptor transcription pathway / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...anatomical structure development / chromatin => GO:0000785 / Regulation of gene expression in beta cells / transcription initiation at RNA polymerase II promoter / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Nuclear Receptor transcription pathway / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / centrosome / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.7 Å | ||||||
Authors | Wisely, B. / Miller, A.B. / Davis, R.G. / Spitzer, T. / Shearer, B. / Moore, J.T. / Johnson, R. / Sefler, A. / Willson, T.M. / Williams, S.P. | ||||||
Citation | Journal: Structure / Year: 2002 Title: Hepatocyte Nuclear Factor 4 Is a Transcription Factor that Constitutively Binds Fatty Acids. Authors: Wisely, G.B. / Miller, A.B. / Davis, R.G. / Jr Thornquest, A.D. / Johnson, R. / Spitzer, T. / Sefler, A. / Shearer, B. / Moore, J.T. / Willson, T.M. / Williams, S.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lv2.cif.gz | 57.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lv2.ent.gz | 41.8 KB | Display | PDB format |
PDBx/mmJSON format | 1lv2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lv2_validation.pdf.gz | 406 KB | Display | wwPDB validaton report |
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Full document | 1lv2_full_validation.pdf.gz | 416.2 KB | Display | |
Data in XML | 1lv2_validation.xml.gz | 7.5 KB | Display | |
Data in CIF | 1lv2_validation.cif.gz | 10.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/1lv2 ftp://data.pdbj.org/pub/pdb/validation_reports/lv/1lv2 | HTTPS FTP |
-Related structure data
Similar structure data |
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-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: 25854.926 Da / Num. of mol.: 1 / Fragment: HNF4g LBD (residues 103-328) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HNF4G / Plasmid: pRSETa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21[DE3] / References: UniProt: Q14541 |
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#2: Chemical | ChemComp-PLM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.27 Å3/Da / Density % sol: 76.64 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: ammonium phosphate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 21K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 5, 2000 / Details: bent silicon crystal |
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: 2.7→22.4 Å / Num. all: 15429 / Num. obs: 15108 / % possible obs: 97.9 % / Observed criterion σ(I): 1 / Redundancy: 15.8 % / Biso Wilson estimate: 67.547 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 36.3 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 15.4 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1846 / Rsym value: 0.4 / % possible all: 99.5 |
Reflection | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 50 Å / Num. obs: 18866 / % possible obs: 98.4 % / Num. measured all: 1308098 |
Reflection shell | *PLUS % possible obs: 93.7 % / Rmerge(I) obs: 0.32 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS Starting model: Built by fitting pieces of secondary structure into density. Resolution: 2.7→19.92 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: CNS
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.1994 Å2 / ksol: 0.339487 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.2 Å2
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Refine analyze | Luzzati coordinate error free: 0.46 Å / Luzzati sigma a free: 0.59 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→19.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 50 Å / % reflection Rfree: 7 % / Rfactor Rfree: 0.268 / Rfactor Rwork: 0.248 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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