[English] 日本語
![](img/lk-miru.gif)
- PDB-5c6v: Crystal structure of the rice Topless related protein 2 (TPR2) N-... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5c6v | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the rice Topless related protein 2 (TPR2) N-terminal domain (1-209) in complex with Arabidopsis NINJA peptide | ||||||||||||
![]() |
| ||||||||||||
![]() | TRANSCRIPTION / transcriptional corepressor / alpha-helical structure / tetrameric protein / plant transcriptional repression / Plant development | ||||||||||||
Function / homology | ![]() positive regulation of pattern recognition receptor signaling pathway / regulation of leaf morphogenesis / jasmonic acid mediated signaling pathway / response to jasmonic acid / protein sequestering activity / defense response / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / nucleus / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Ke, J. / Ma, H. / Gu, X. / Brunzelle, J.S. / Xu, H.E. / Melcher, K. | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: Structural basis for recognition of diverse transcriptional repressors by the TOPLESS family of corepressors. Authors: Ke, J. / Ma, H. / Gu, X. / Thelen, A. / Brunzelle, J.S. / Li, J. / Xu, H.E. / Melcher, K. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 177.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 142.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 482 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 493.3 KB | Display | |
Data in XML | ![]() | 29.9 KB | Display | |
Data in CIF | ![]() | 40.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4zheSC ![]() 5c6qC ![]() 5c7eC ![]() 5c7fC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 24903.611 Da / Num. of mol.: 4 / Fragment: N-terminal domain (UNP residues 1-209) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 1117.210 Da / Num. of mol.: 4 / Fragment: UNP residues 4-14 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55.5 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% w/v PEG 3,350, 0.2 M NaCl, 0.1 M BIS-TRIS pH 5.5, 3.0% w/v D-(+)-glucose monohydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 14, 2014 |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.078 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. all: 20063 / Num. obs: 20063 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.172 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 3.1→3.31 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4ZHE Resolution: 3.1→48.495 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 34.23 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→48.495 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|