+Open data
-Basic information
Entry | Database: PDB / ID: 1g39 | ||||||
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Title | WILD-TYPE HNF-1ALPHA DIMERIZATION DOMAIN | ||||||
Components | HEPATOCYTE NUCLEAR FACTOR 1-ALPHA | ||||||
Keywords | TRANSCRIPTION / dimerization domain / four-helix bundle / transcription factor | ||||||
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 / reproductive structure development / bile acid biosynthetic process / 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 / reproductive structure development / bile acid biosynthetic process / cellular response to L-leucine / reverse cholesterol transport / bile acid and bile salt transport / pronucleus / pancreas development / negative regulation of miRNA processing / insulin secretion / regulation of Wnt signaling pathway / positive regulation of mitochondrial membrane potential / embryonic limb morphogenesis / 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 / positive regulation of insulin secretion / transcription coactivator binding / 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 / transcription cis-regulatory region binding / protein dimerization activity / 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 / MOLECULAR REPLACEMENT / Resolution: 1.22 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 | 1g39.cif.gz | 35.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g39.ent.gz | 26.6 KB | Display | PDB format |
PDBx/mmJSON format | 1g39.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/1g39 ftp://data.pdbj.org/pub/pdb/validation_reports/g3/1g39 | 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: 3386.951 Da / Num. of mol.: 4 / Fragment: DIMERIZATION DOMAIN, RESIDUE 1-32 / Source method: obtained synthetically Details: This peptide was chemically synthesized. The sequence of this peptide naturally occurs in mouse (Mus musculus). 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: 2.3 Å3/Da / Density % sol: 46.59 % | ||||||||||||||||||||||||||||||
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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: SSRL / Beamline: BL9-2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 24, 2000 / Details: Double crystal |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.22→20.6 Å / Num. all: 19878 / Num. obs: 36802 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 24.6 |
Reflection shell | Resolution: 1.22→1.28 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1952 / % possible all: 100 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.497 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: peptide model with selenomethionine substituted at position 12, solved by MAD Resolution: 1.22→20.6 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 581513.8 / 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: 55.24 Å2 / ksol: 0.421 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.22→20.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.22→1.28 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20.6 Å / σ(F): 0 / % reflection Rfree: 5.8 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 22.7 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.44 / % reflection Rfree: 5.8 % / Rfactor Rwork: 0.42 |