[English] 日本語
![](img/lk-miru.gif)
- PDB-3d24: Crystal structure of ligand-binding domain of estrogen-related re... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3d24 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of ligand-binding domain of estrogen-related receptor alpha (ERRalpha) in complex with the peroxisome proliferators-activated receptor coactivator-1alpha box3 peptide (PGC-1alpha) | ||||||
![]() |
| ||||||
![]() | TRANSCRIPTION / nuclear receptor / ligand binding domain / coactivator / DNA-binding / Metal-binding / Nucleus / Phosphoprotein / Transcription regulation / Zinc / Zinc-finger / Polymorphism / RNA-binding / Structural Genomics / Structural Proteomics in Europe / SPINE | ||||||
Function / homology | ![]() positive regulation of fatty acid oxidation / : / lncRNA binding / response to muscle activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / cellular respiration / nuclear steroid receptor activity / temperature homeostasis / intercellular bridge / intracellular glucose homeostasis ...positive regulation of fatty acid oxidation / : / lncRNA binding / response to muscle activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / cellular respiration / nuclear steroid receptor activity / temperature homeostasis / intercellular bridge / intracellular glucose homeostasis / response to starvation / fatty acid oxidation / response to dietary excess / estrogen response element binding / adipose tissue development / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / energy homeostasis / brown fat cell differentiation / nuclear receptor-mediated steroid hormone signaling pathway / positive regulation of gluconeogenesis / digestion / steroid binding / respiratory electron transport chain / mitochondrion organization / RNA splicing / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / gluconeogenesis / nuclear receptor binding / transcription initiation at RNA polymerase II promoter / transcription coregulator activity / negative regulation of smooth muscle cell proliferation / circadian regulation of gene expression / Heme signaling / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / PPARA activates gene expression / chromatin DNA binding / mRNA processing / PML body / fibrillar center / positive regulation of DNA-binding transcription factor activity / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / Regulation of RUNX2 expression and activity / nuclear receptor activity / microtubule cytoskeleton / sequence-specific double-stranded DNA binding / Circadian Clock / positive regulation of cold-induced thermogenesis / cellular response to oxidative stress / protein-containing complex assembly / DNA-binding transcription factor binding / neuron apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of neuron apoptotic process / sequence-specific DNA binding / transcription coactivator activity / protein stabilization / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / protein domain specific binding / ubiquitin protein ligase binding / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Moras, D. / Greschik, H. / Flaig, R. / Sato, Y. / Rochel, N. / Structural Proteomics in Europe (SPINE) | ||||||
![]() | ![]() Title: Communication between the ERR{alpha} Homodimer Interface and the PGC-1{alpha} Binding Surface via the Helix 8-9 Loop. Authors: Greschik, H. / Althage, M. / Flaig, R. / Sato, Y. / Chavant, V. / Peluso-Iltis, C. / Choulier, L. / Cronet, P. / Rochel, N. / Schule, R. / Stromstedt, P.E. / Moras, D. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 106.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 81.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 477 KB | Display | |
Data in XML | ![]() | 22.6 KB | Display | |
Data in CIF | ![]() | 32 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1xb7S S: Starting model for refinement |
---|---|
Similar structure data | |
Other databases |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
| ||||||||
Details | AUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS A HOMODIMER. |
-
Components
#1: Protein | Mass: 27584.893 Da / Num. of mol.: 2 / Fragment: Ligand binding domain: Residues 278-519 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 2665.975 Da / Num. of mol.: 2 / Fragment: Residues 198-219 / Source method: obtained synthetically Details: Synthetic peptide with the sequence based on the fragment (residues 198-219) of human PGC-1-alpha, UniProt entry Q9UBK2 (PRGC1_HUMAN) References: UniProt: Q9UBK2 #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.28 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M Bis-Tris pH 5.5, 15% PEG 3350, 0.2 M Mg(NO3)2, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 13, 2007 / Details: Toroidal Zerodur mirror |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→50 Å / Num. all: 111465 / Num. obs: 109542 / % possible obs: 88.9 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 29.7 Å2 / Rsym value: 0.031 / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 2.11→2.19 Å / Redundancy: 3.2 % / Num. unique all: 2740 / Rsym value: 0.238 / % possible all: 76.9 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 1XB7 Resolution: 2.11→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: The Bijvoet differences were used in phasing
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.5 Å2
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.11→50 Å
| |||||||||||||||||||||||||
Refine LS restraints |
|