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Yorodumi- PDB-1g2y: HNF-1ALPHA DIMERIZATION DOMAIN, WITH SELENOMETHIONINE SUBSTITUED ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g2y | ||||||
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Title | HNF-1ALPHA DIMERIZATION DOMAIN, WITH SELENOMETHIONINE SUBSTITUED AT LEU 12 | ||||||
Components | HEPATOCYTE NUCLEAR FACTOR 1-ALPHA | ||||||
Keywords | TRANSCRIPTION / dimerization domain / four-helix bundle / transcription factor / selenomethionine | ||||||
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 / reverse cholesterol transport / cellular response to L-leucine ...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 / reverse cholesterol transport / cellular response to L-leucine / 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 / protein dimerization activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1 Å | ||||||
Authors | Rose, R.B. / Endrizzi, J.A. / Cronk, J.D. / Holton, J. / Alber, T. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: High-resolution structure of the HNF-1alpha dimerization domain. Authors: Rose, R.B. / Endrizzi, J.A. / Cronk, J.D. / Holton, J. / Alber, T. #1: Journal: Nat.Struct.Biol. / Year: 2000 Title: Structural basis of dimerization, coactivator recognition and MODY3 mutations in HNF-1alpha Authors: Rose, R.B. / Bayle, J.H. / Endrizzi, J.A. / Cronk, J.D. / Crabtree, G.R. / Alber, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g2y.cif.gz | 35.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g2y.ent.gz | 26.5 KB | Display | PDB format |
PDBx/mmJSON format | 1g2y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/1g2y ftp://data.pdbj.org/pub/pdb/validation_reports/g2/1g2y | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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Details | There are two HNF-1alpha dimers in the asymmetric unit: monomers A and C, and monomers B and D. |
-Components
#1: Protein/peptide | Mass: 3451.884 Da / Num. of mol.: 4 / Fragment: DIMERIZATION DOMAIN, RESIDUES 1-32 / Mutation: L12(MSE) / Source method: obtained synthetically Details: This peptide was chemically synthesized. The sequence of this peptide naturally occurs in mouse (Mus musculus), with a point mutation at position 12. References: UniProt: P22361 #2: 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: 2.19 Å3/Da / Density % sol: 43.83 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, Tris-HCl, lithium sulphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 200 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.95372, 0.97957, 0.9798, 1.07812 | |||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 28, 1999 / Details: Double crystal | |||||||||||||||
Radiation | Monochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1→30.9 Å / Num. all: 55221 / Num. obs: 55221 / % possible obs: 86.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Biso Wilson estimate: 7.4 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 16.8 | |||||||||||||||
Reflection shell | Resolution: 1→1.05 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.101 / Mean I/σ(I) obs: 9.2 / Num. unique all: 55221 / % possible all: 73.1 | |||||||||||||||
Reflection | *PLUS | |||||||||||||||
Reflection shell | *PLUS % possible obs: 73.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: wARP model Resolution: 1→30.88 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 499172.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 98.59 Å2 / ksol: 0.372 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1→30.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1→1.06 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / Num. reflection Rfree: 5640 / % reflection Rfree: 9 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 16 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.375 / % reflection Rfree: 2.9 % / Rfactor Rwork: 0.398 |