[English] 日本語
![](img/lk-miru.gif)
- PDB-3i91: Crystal structure of human chromobox homolog 8 (CBX8) with H3K9 p... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3i91 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human chromobox homolog 8 (CBX8) with H3K9 peptide | ||||||
![]() |
| ||||||
![]() | TRANSCRIPTION / Chromobox homolog 8 / CBX8 / H3K9 peptide / Structural Genomics / Structural Genomics Consortium / SGC / Chromatin regulator / Nucleus / Phosphoprotein / Repressor / Transcription regulation | ||||||
Function / homology | ![]() PRC1 complex / ubiquitin-protein transferase activator activity / PcG protein complex / SUMOylation of DNA methylation proteins / SUMOylation of RNA binding proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of collagen biosynthetic process / heterochromatin / SUMOylation of DNA damage response and repair proteins / methylated histone binding ...PRC1 complex / ubiquitin-protein transferase activator activity / PcG protein complex / SUMOylation of DNA methylation proteins / SUMOylation of RNA binding proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of collagen biosynthetic process / heterochromatin / SUMOylation of DNA damage response and repair proteins / methylated histone binding / positive regulation of DNA repair / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / Regulation of PTEN gene transcription / cellular response to hydrogen peroxide / chromatin organization / Oxidative Stress Induced Senescence / single-stranded RNA binding / chromatin binding / positive regulation of cell population proliferation / chromatin / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Amaya, M.F. / Ravichandran, M. / Loppnau, P. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Min, J. ...Amaya, M.F. / Ravichandran, M. / Loppnau, P. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Min, J. / Ouyang, H. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Recognition and specificity determinants of the human cbx chromodomains. Authors: Kaustov, L. / Ouyang, H. / Amaya, M. / Lemak, A. / Nady, N. / Duan, S. / Wasney, G.A. / Li, Z. / Vedadi, M. / Schapira, M. / Min, J. / Arrowsmith, C.H. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 38 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 29.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 445.8 KB | Display | |
Data in XML | ![]() | 10.4 KB | Display | |
Data in CIF | ![]() | 14.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2l11C ![]() 2l12C ![]() 2l1bC ![]() 3fdtC ![]() 3gv6C ![]() 3h91C ![]() 3i90C ![]() 3i8y C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 6610.602 Da / Num. of mol.: 2 / Fragment: Chromo domain: UNP residues 8-61 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | | Mass: 892.013 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.68 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7 / Details: pH 7.0, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD Details: Cryo-cooled first crystal and sagitally focusing second crystal |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. obs: 23019 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: REFINED INDIVIDUALLY.
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.95 Å2 / Biso mean: 19.565 Å2 / Biso min: 6.53 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→50 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
|