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Yorodumi- PDB-4ywc: Crystal structure of Myc3(5-242) fragment in complex with Jaz9(21... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ywc | |||||||||
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Title | Crystal structure of Myc3(5-242) fragment in complex with Jaz9(218-239) peptide | |||||||||
Components |
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Keywords | TRANSCRIPTION REGULATOR / helix-sheet-helix sandwich fold / Jasmonate signaling / Myc transcription factor / Myc-Jaz complex | |||||||||
Function / homology | Function and homology information extracellular ATP signaling / anthocyanin-containing compound biosynthetic process / stomatal complex development / response to jasmonic acid / bHLH transcription factor binding / defense response / protein dimerization activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription ...extracellular ATP signaling / anthocyanin-containing compound biosynthetic process / stomatal complex development / response to jasmonic acid / bHLH transcription factor binding / defense response / protein dimerization activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / 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. / Xu, H.E. / Melcher, K. / He, S.Y. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nature / Year: 2015 Title: Structural basis of JAZ repression of MYC transcription factors in jasmonate signalling. Authors: Zhang, F. / Yao, J. / Ke, J. / Zhang, L. / Lam, V.Q. / Xin, X.F. / Zhou, X.E. / Chen, J. / Brunzelle, J. / Griffin, P.R. / Zhou, M. / Xu, H.E. / Melcher, K. / He, S.Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ywc.cif.gz | 94.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ywc.ent.gz | 70.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ywc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ywc_validation.pdf.gz | 456.5 KB | Display | wwPDB validaton report |
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Full document | 4ywc_full_validation.pdf.gz | 464.3 KB | Display | |
Data in XML | 4ywc_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 4ywc_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/4ywc ftp://data.pdbj.org/pub/pdb/validation_reports/yw/4ywc | HTTPS FTP |
-Related structure data
Related structure data | 4rqwC 4rruSC 4rs9C 4yz6C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25954.275 Da / Num. of mol.: 2 / Fragment: N-terminal domain (UNP residues 5-242) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MYC3, ATR2, BHLH5, EN36, At5g46760, MZA15.18 / Plasmid: pSUMO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9FIP9 #2: Protein/peptide | Mass: 2622.164 Da / Num. of mol.: 2 / Fragment: UNP residues 194-215 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: Q8W4J8 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.86 % / Description: plate shaped crystals |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.9 Details: The purified proteins at a concentration of 15 mg/ml are mixed with 0.2 M magnesium nitrate, 20% (w/v) polyethylene glycol 3,350. Crystals of about 100 um in length appeared in 3 days |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 13, 2015 |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 21208 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 8.3 % / Rmerge(I) obs: 1.07 / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4RRU Resolution: 2.4→49.621 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.04 / Stereochemistry target values: ML
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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→49.621 Å
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Refine LS restraints |
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LS refinement shell |
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