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- PDB-1f93: CRYSTAL STRUCTURE OF A COMPLEX BETWEEN THE DIMERIZATION DOMAIN OF... -
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Basic information
Entry | Database: PDB / ID: 1f93 | ||||||
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Title | CRYSTAL STRUCTURE OF A COMPLEX BETWEEN THE DIMERIZATION DOMAIN OF HNF-1 ALPHA AND THE COACTIVATOR DCOH | ||||||
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![]() | TRANSCRIPTION / four-helix bundle / transcriptional activator-coactivator complex / dimerization domain | ||||||
Function / homology | ![]() paraxial mesoderm formation / Phenylalanine metabolism / 4a-hydroxytetrahydrobiopterin dehydratase / 4-alpha-hydroxytetrahydrobiopterin dehydratase activity / cellular response to rapamycin / apoptotic nuclear changes / L-phenylalanine metabolic process / regulation of NADP metabolic process / renal glucose absorption / phenylalanine 4-monooxygenase activity ...paraxial mesoderm formation / Phenylalanine metabolism / 4a-hydroxytetrahydrobiopterin dehydratase / 4-alpha-hydroxytetrahydrobiopterin dehydratase activity / cellular response to rapamycin / apoptotic nuclear changes / L-phenylalanine metabolic process / regulation of NADP metabolic process / renal glucose absorption / phenylalanine 4-monooxygenase activity / regulation of hormone secretion / reproductive structure development / regulation of protein binding / bile acid biosynthetic process / cellular response to L-leucine / tetrahydrobiopterin biosynthetic process / 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 / cholesterol metabolic process / liver development / transcription coregulator binding / cellular response to glucose stimulus / placenta development / positive regulation of insulin secretion / transcription coactivator binding / fatty acid biosynthetic process / protein localization / 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 / transcription coactivator activity / 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 / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / 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 / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Rose, R.B. / Bayle, J.H. / Endrizzi, J.A. / Cronk, J.D. / Crabtree, G.R. / Alber, T. | ||||||
![]() | ![]() 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. #1: ![]() Title: Crystal structure of DCoH, a bifunctional, protein-binding transcriptional coactivator Authors: Endrizzi, J.A. / Cronk, J.D. / Weidong, W. / Crabtree, G.R. / Alber, T. #2: ![]() Title: High-resolution structures of the bifunctional enzyme and transcriptional coactivator DCoH and its complex with a product analogue Authors: Cronk, J.D. / Endrizzi, J.A. / Alber, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 108.2 KB | Display | ![]() |
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PDB format | ![]() | 89.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | The biological assembly is a heterotetramer consisting of a DCoH dimer and an HNF-1 alpha dimerization domain dimer. There are two heterotetramers in the asymmetric unit. |
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Components
#1: Protein | Mass: 12158.288 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 3386.951 Da / Num. of mol.: 4 / Fragment: DIMERIZATION DOMAIN (RESIDUES 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 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.61 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG 8000, potassium succinate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion / Details: used microseeding | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM / Detector: CCD / Date: Jan 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0688 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. all: 59400 / Num. obs: 16500 / % possible obs: 95 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 43.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22 |
Reflection shell | Resolution: 2.6→2.67 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.3 / Num. unique all: 1800 / % possible all: 95 |
Reflection | *PLUS % possible obs: 95 % / Num. measured all: 59400 / Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS % possible obs: 95 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 2.6 |
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Processing
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Refinement | Resolution: 2.6→20.1 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 912032.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber / Details: used non-crystallographic symmetry
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.35 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→20.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 7.8 % | ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 58.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.371 / % reflection Rfree: 8 % / Rfactor Rwork: 0.31 |