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- PDB-5ja5: Crystal structure of the rice Topless related protein 2 (TPR2) N-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ja5 | ||||||||||||
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Title | Crystal structure of the rice Topless related protein 2 (TPR2) N-terminal topless domain (1-209) L111A and L130A mutant in complex with rice D53 repressor EAR peptide motif | ||||||||||||
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![]() | TRANSCRIPTION / TRANSCRIPTION REPRESSION / TRANSCRIPTIONAL COREPRESSOR TOPLESS / ALPHA-HELICAL STRUCTURE / TETRAMER / TRANSCRIPTIONAL REPRESSOR D53 | ||||||||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Ke, J. / Ma, H. / Gu, X. / Brunzelle, J.S. / Xu, H.E. / Melcher, K. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62.5 KB | Display | ![]() |
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PDB format | ![]() | 44 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.8 KB | Display | ![]() |
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Full document | ![]() | 438.6 KB | Display | |
Data in XML | ![]() | 11.3 KB | Display | |
Data in CIF | ![]() | 15.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5j9kC ![]() 5jgcC ![]() 5jhpC ![]() 4zheS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24819.451 Da / Num. of mol.: 1 / Fragment: N-terminal topless domain (UNP residues 1-209) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: TPR1, ASPR2, TPR2, Os01g0254100, LOC_Os01g15020, OsJ_01134, OSNPB_010254100, P0705D01.10-1 Production host: ![]() ![]() |
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#2: Protein/peptide | Mass: 1864.961 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8 Details: 20% w/v Polyethylene glycol 3350, 0.2 M Potassium phosphate monobasic, pH 4.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: liquid nitrogen stream |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 7, 2015 |
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: 2→50 Å / Num. obs: 20502 / % possible obs: 100 % / Redundancy: 15.6 % / CC1/2: 1 / Rmerge(I) obs: 0.07 / Net I/σ(I): 25.9 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 16 % / Rmerge(I) obs: 0.893 / Mean I/σ(I) obs: 4 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ZHE Resolution: 2→29.612 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 23.79
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→29.612 Å
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Refine LS restraints |
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LS refinement shell |
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