+Open data
-Basic information
Entry | Database: PDB / ID: 1jb6 | ||||||
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Title | Crystal Structure of Dimerization Domain (1-33) of HNF-1alpha | ||||||
Components | HEPATOCYTE NUCLEAR FACTOR 1-ALPHA | ||||||
Keywords | TRANSCRIPTION / Four-helix bundle / non-canonical turn | ||||||
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 / pronucleus / bile acid and bile salt transport / regulation of Wnt signaling pathway / pancreas development / negative regulation of miRNA processing / positive regulation of mitochondrial membrane potential / insulin secretion / embryonic limb morphogenesis / heme biosynthetic process / positive regulation of ATP biosynthetic process / negative regulation of peptidyl-threonine phosphorylation / glucose import / blastocyst development / photoreceptor outer segment / fatty acid transport / bone resorption / response to glucose / transcription coregulator binding / cholesterol metabolic process / liver development / placenta development / cellular response to glucose stimulus / positive regulation of insulin secretion / fatty acid biosynthetic process / transcription coactivator binding / protein localization / glucose homeostasis / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA binding / response to oxidative stress / transcription cis-regulatory region binding / transcription by RNA polymerase II / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / protein dimerization activity / positive regulation of protein phosphorylation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of gene expression / positive regulation of DNA-templated transcription / chromatin / negative regulation of apoptotic process / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / 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: 1.7 Å | ||||||
Authors | Narayana, N. / Hua, Q.-X. / Weiss, M.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: The dimerization domain of HNF-1alpha: structure and plasticity of an intertwined four-helix bundle with application to diabetes mellitus. Authors: Narayana, N. / Hua, Q. / Weiss, M.A. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: Diabetes-Associated Mutations in a beta-Cell Transcription factor Destabilize an Antiparallel "Mini-Zipper" in a Dimerization Interface Authors: Hua, Q.X. / Zhao, M. / Narayana, N. / Nakagawa, S.H. / Jia, W. / Weiss, M.A. #2: 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. #3: 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. #4: Journal: BIO*ESSAYS / Year: 1992 Title: HNF1, A Homeoprotein Member of the Hepatic Transcription Regulatory Network Authors: Tronche, F. / Yaniv, M. #5: Journal: DIABETES METAB. / Year: 1997 Title: Maturity-onset Diabetes of the Young (MODY), MODY Genes and Non-Insulin-Dependent Diabetes mellitus Authors: Velho, G. / Froguel, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jb6.cif.gz | 20.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jb6.ent.gz | 15.9 KB | Display | PDB format |
PDBx/mmJSON format | 1jb6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jb6_validation.pdf.gz | 429.9 KB | Display | wwPDB validaton report |
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Full document | 1jb6_full_validation.pdf.gz | 430.1 KB | Display | |
Data in XML | 1jb6_validation.xml.gz | 5.3 KB | Display | |
Data in CIF | 1jb6_validation.cif.gz | 6.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/1jb6 ftp://data.pdbj.org/pub/pdb/validation_reports/jb/1jb6 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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 independent molecules in the asymmetric unit. For each molecule, a crystallographic 2-fold axis generates the biological dimer. |
-Components
#1: Protein/peptide | Mass: 3620.056 Da / Num. of mol.: 2 / Fragment: Dimerization domain (residues 1-32) / Source method: obtained synthetically Details: This peptide was chemically synthesized. The sequence of this peptide occurs naturally in Mus musculus (mouse) as well as in Homo sapiens (humans). 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: 1.6 Å3/Da / Density % sol: 23 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: MPD, Tris-HCl, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 | |||||||||||||||||||||||||||||||||||
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: 19-ID / Wavelength: 0.9794, 0.9800, 1.0030 | ||||||||||||
Detector | Type: SBC-2 / Detector: CCD / Date: Mar 24, 2000 / Details: mirrors | ||||||||||||
Radiation | Monochromator: Double Crystal Silicon / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.7→40 Å / Num. all: 5922 / Num. obs: 5245 / % possible obs: 88 % / Observed criterion σ(F): 3 / Redundancy: 6 % / Rsym value: 0.037 | ||||||||||||
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 5 % / Num. unique all: 584 / Rsym value: 0.024 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.7→40 Å / σ(F): 3
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Refinement step | Cycle: LAST / Resolution: 1.7→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.78 Å
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 40 Å / σ(F): 3 / % reflection Rfree: 5 % / Rfactor obs: 0.231 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.262 / Rfactor Rwork: 0.22 |