[English] 日本語
Yorodumi- PDB-5t0f: Crystal structure of the Myc3 N-terminal domain [44-242] in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5t0f | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the Myc3 N-terminal domain [44-242] in complex with JAZ10 CMID domain [16-58] from arabidopsis | ||||||||||||
Components |
| ||||||||||||
Keywords | TRANSCRIPTION / transcriptional repression / jasmonate signaling / MYC3 / JAZ10 CMID / alternative splicing / desensitization | ||||||||||||
Function / homology | Function and homology information regulation of defense response / regulation of systemic acquired resistance / regulation of jasmonic acid mediated signaling pathway / extracellular ATP signaling / anthocyanin-containing compound biosynthetic process / stomatal complex development / response to jasmonic acid / bHLH transcription factor binding / defense response / response to wounding ...regulation of defense response / regulation of systemic acquired resistance / regulation of jasmonic acid mediated signaling pathway / extracellular ATP signaling / anthocyanin-containing compound biosynthetic process / stomatal complex development / response to jasmonic acid / bHLH transcription factor binding / defense response / response to wounding / protein dimerization activity / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / nucleus Similarity search - Function | ||||||||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||||||||
Authors | Ke, J. / Zhang, F. / Brunzelle, J.S. / He, S.Y. / Xu, H.E. / Melcher, K. | ||||||||||||
Funding support | United States, 3items
| ||||||||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Structural insights into alternative splicing-mediated desensitization of jasmonate signaling. Authors: Zhang, F. / Ke, J. / Zhang, L. / Chen, R. / Sugimoto, K. / Howe, G.A. / Xu, H.E. / Zhou, M. / He, S.Y. / Melcher, K. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5t0f.cif.gz | 54.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5t0f.ent.gz | 37.2 KB | Display | PDB format |
PDBx/mmJSON format | 5t0f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5t0f_validation.pdf.gz | 431.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5t0f_full_validation.pdf.gz | 432.8 KB | Display | |
Data in XML | 5t0f_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 5t0f_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t0/5t0f ftp://data.pdbj.org/pub/pdb/validation_reports/t0/5t0f | HTTPS FTP |
-Related structure data
Related structure data | 5t0qC 4rqwS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
| ||||||||
Details | dimer according to size exclusion chromatography |
-Components
#1: Protein | Mass: 21872.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MYC3, ATR2, BHLH5, EN36, At5g46760, MZA15.18 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FIP9 |
---|---|
#2: Protein/peptide | Mass: 4967.769 Da / Num. of mol.: 1 / Fragment: UNP residues 16-58 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TIFY9, JAS1, JAZ10, At5g13220, T31B5.40 / Production host: Escherichia coli (E. coli) / References: UniProt: Q93ZM9 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.91 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1 M Tris, pH 6.0, 20% (w/v) polyethylene glycol monomethyl ether 2,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: liquid nitrogen |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 14, 2015 |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 9574 / % possible obs: 100 % / Redundancy: 14.3 % / CC1/2: 1 / Rmerge(I) obs: 0.067 / Net I/σ(I): 26.1 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 14.9 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 3.5 / CC1/2: 0.935 / % possible all: 99.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4RQW Resolution: 2.4→31.632 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 30.61 / 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: 2.4→31.632 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|