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Yorodumi- PDB-1lfb: THE X-RAY STRUCTURE OF AN ATYPICAL HOMEODOMAIN PRESENT IN THE RAT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lfb | ||||||
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Title | THE X-RAY STRUCTURE OF AN ATYPICAL HOMEODOMAIN PRESENT IN THE RAT LIVER TRANSCRIPTION FACTOR LFB1(SLASH)HNF1 AND IMPLICATIONS FOR DNA BINDING | ||||||
Components | LIVER TRANSCRIPTION FACTOR (LFB1) | ||||||
Keywords | TRANSCRIPTION REGULATION | ||||||
Function / homology | Function and homology information paraxial mesoderm formation / cellular response to rapamycin / apoptotic nuclear changes / regulation of NADP metabolic process / renal glucose absorption / regulation of hormone secretion / bile acid biosynthetic process / reproductive structure development / cellular response to L-leucine / reverse cholesterol transport ...paraxial mesoderm formation / cellular response to rapamycin / apoptotic nuclear changes / regulation of NADP metabolic process / renal glucose absorption / regulation of hormone secretion / bile acid biosynthetic process / reproductive structure development / cellular response to L-leucine / reverse cholesterol transport / bile acid and bile salt transport / pronucleus / pancreas development / positive regulation of mitochondrial membrane potential / negative regulation of miRNA processing / embryonic limb morphogenesis / regulation of Wnt signaling pathway / insulin secretion / heme biosynthetic process / positive regulation of ATP biosynthetic process / glucose import / negative regulation of peptidyl-threonine phosphorylation / blastocyst development / photoreceptor outer segment / positive regulation of transcription initiation by RNA polymerase II / fatty acid transport / response to glucose / bone resorption / cholesterol metabolic process / liver development / placenta development / transcription coregulator binding / cellular response to glucose stimulus / protein localization / transcription coactivator binding / positive regulation of insulin secretion / fatty acid biosynthetic process / glucose homeostasis / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / response to oxidative stress / transcription regulator complex / sequence-specific DNA binding / transcription by RNA polymerase II / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein dimerization activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / positive regulation of protein phosphorylation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / chromatin binding / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / 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 / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.8 Å | ||||||
Authors | Ceska, T.A. / Lamers, M. / Monaci, P. / Nicosia, A. / Cortese, R. / Suck, D. | ||||||
Citation | Journal: EMBO J. / Year: 1993 Title: The X-ray structure of an atypical homeodomain present in the rat liver transcription factor LFB1/HNF1 and implications for DNA binding. Authors: Ceska, T.A. / Lamers, M. / Monaci, P. / Nicosia, A. / Cortese, R. / Suck, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lfb.cif.gz | 26.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lfb.ent.gz | 17.3 KB | Display | PDB format |
PDBx/mmJSON format | 1lfb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lf/1lfb ftp://data.pdbj.org/pub/pdb/validation_reports/lf/1lfb | HTTPS FTP |
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-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
#1: Protein | Mass: 11677.199 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: LIVER / References: UniProt: P22361, UniProt: P15257*PLUS |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.4 % | |||||||||||||||
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Crystal | *PLUS Density % sol: 65 % | |||||||||||||||
Crystal grow | *PLUS pH: 5 / Method: vapor diffusion, hanging drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.8 Å / Num. all: 43872 / Num. obs: 4344 |
-Processing
Software |
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Refinement | Resolution: 2.8→6 Å
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Refinement step | Cycle: LAST / Resolution: 2.8→6 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 6 Å / Num. reflection obs: 2487 / Rfactor obs: 0.212 / Rfactor Rfree: 0.364 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.36 |