[English] 日本語
Yorodumi- PDB-5j9k: Crystal structure of the rice Topless related protein 2 (TPR2) N-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5j9k | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the rice Topless related protein 2 (TPR2) N-terminal topless domain (1-209) in complex with rice D53 repressor EAR peptide motif | ||||||||||||
Components |
| ||||||||||||
Keywords | TRANSCRIPTION / TRANSCRIPTION REPRESSION / TRANSCRIPTIONAL COREPRESSOR TOPLESS / ALPHA-HELICAL STRUCTURE / TETRAMER / TRANSCRIPTIONAL REPRESSOR D53 | ||||||||||||
Function / homology | Function and homology information positive regulation of pattern recognition receptor signaling pathway / response to strigolactone / protein sequestering activity / regulation of DNA-templated transcription / nucleus / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Oryza sativa (Asian cultivated rice) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.55 Å | ||||||||||||
Authors | Ke, J. / Ma, H. / Gu, X. / Brunzelle, J.S. / Xu, H.E. / Melcher, K. | ||||||||||||
Funding support | United States, 3items
| ||||||||||||
Citation | Journal: Sci Adv / Year: 2017 Title: A D53 repression motif induces oligomerization of TOPLESS corepressors and promotes assembly of a corepressor-nucleosome complex. Authors: Ma, H. / Duan, J. / Ke, J. / He, Y. / Gu, X. / Xu, T.H. / Yu, H. / Wang, Y. / Brunzelle, J.S. / Jiang, Y. / Rothbart, S.B. / Xu, H.E. / Li, J. / Melcher, K. #1: Journal: Sci Adv / Year: 2015 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: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5j9k.cif.gz | 102.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5j9k.ent.gz | 79.4 KB | Display | PDB format |
PDBx/mmJSON format | 5j9k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5j9k_validation.pdf.gz | 450.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5j9k_full_validation.pdf.gz | 457.6 KB | Display | |
Data in XML | 5j9k_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 5j9k_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/5j9k ftp://data.pdbj.org/pub/pdb/validation_reports/j9/5j9k | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 24903.611 Da / Num. of mol.: 2 / Fragment: N-terminal topless domain (UNP residues 1-209) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa (Asian cultivated rice) Gene: TPR1, ASPR2, TPR2, Os01g0254100, LOC_Os01g15020, OsJ_01134, OSNPB_010254100, P0705D01.10-1 Production host: Escherichia coli (E. coli) / References: UniProt: Q5NBT9 #2: Protein/peptide | Mass: 1864.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: DNLIYLDLNLQ / Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Production host: Escherichia coli (E. coli) / References: UniProt: Q2RBP2*PLUS #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.53 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25% w/v Polyethylene glycol 3350, 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: liquid nitrogen |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.033 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 9, 2013 |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→50 Å / Num. obs: 19882 / % possible obs: 99.4 % / Redundancy: 8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.55→2.69 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.949 / Mean I/σ(I) obs: 2 / % possible all: 99.2 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.55→34.377 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.04 / 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: 2.55→34.377 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|