+
Open data
-
Basic information
Entry | Database: PDB / ID: 1g39 | ||||||
---|---|---|---|---|---|---|---|
Title | WILD-TYPE HNF-1ALPHA DIMERIZATION DOMAIN | ||||||
![]() | HEPATOCYTE NUCLEAR FACTOR 1-ALPHA | ||||||
![]() | TRANSCRIPTION / dimerization domain / four-helix bundle / transcription factor | ||||||
Function / homology | ![]() 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 / cellular response to L-leucine / bile acid biosynthetic process / 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 / cellular response to L-leucine / bile acid 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 / embryonic limb morphogenesis / insulin secretion / 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 / response to glucose / bone resorption / cholesterol metabolic process / liver development / transcription coregulator binding / cellular response to glucose stimulus / placenta development / protein localization / positive regulation of insulin secretion / fatty acid biosynthetic process / transcription coactivator binding / 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 / 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 | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rose, R.B. / Endrizzi, J.A. / Cronk, J.D. / Holton, J. / Alber, T. | ||||||
![]() | ![]() 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: ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 35.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 26.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 456.3 KB | Display | |
Data in XML | ![]() | 9.8 KB | Display | |
Data in CIF | ![]() | 13.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 |
| ||||||||
4 | ![]()
| ||||||||
Unit cell |
| ||||||||
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 / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.59 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 200 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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 |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() 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
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.24 Å2 / ksol: 0.421 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.7 Å2
| ||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.22→20.6 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.22→1.28 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.44 / % reflection Rfree: 5.8 % / Rfactor Rwork: 0.42 |