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Yorodumi- PDB-4m7e: Structural insight into BL-induced activation of the BRI1-BAK1 complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 4m7e | |||||||||
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Title | Structural insight into BL-induced activation of the BRI1-BAK1 complex | |||||||||
Components |
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Keywords | TRANSFERASE / phytohormone / brassinosteroid-insensitive 1 / leucine-rich repeat / receptor-like kinases | |||||||||
Function / homology | Function and homology information detection of brassinosteroid stimulus / brassinosteroid homeostasis / anther wall tapetum cell differentiation / pollen exine formation / seedling development / skotomorphogenesis / positive regulation of flower development / brassinosteroid mediated signaling pathway / leaf development / receptor serine/threonine kinase binding ...detection of brassinosteroid stimulus / brassinosteroid homeostasis / anther wall tapetum cell differentiation / pollen exine formation / seedling development / skotomorphogenesis / positive regulation of flower development / brassinosteroid mediated signaling pathway / leaf development / receptor serine/threonine kinase binding / microtubule bundle formation / response to UV-B / steroid binding / transmembrane receptor protein tyrosine kinase activity / defense response / receptor protein-tyrosine kinase / endosome membrane / non-specific serine/threonine protein kinase / endosome / protein kinase activity / protein heterodimerization activity / phosphorylation / signaling receptor binding / protein serine kinase activity / protein serine/threonine kinase activity / protein homodimerization activity / protein-containing complex / ATP binding / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.602 Å | |||||||||
Authors | Chai, J. / Han, Z. / Sun, Y. | |||||||||
Citation | Journal: To be Published Title: Structural insight into BL-induced activation of the BRI1-BAK1 complex Authors: Sun, Y. / Han, Z. / Chai, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4m7e.cif.gz | 351.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m7e.ent.gz | 283.6 KB | Display | PDB format |
PDBx/mmJSON format | 4m7e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m7/4m7e ftp://data.pdbj.org/pub/pdb/validation_reports/m7/4m7e | HTTPS FTP |
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-Related structure data
Related structure data | 3rgzS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ABDC
#1: Protein | Mass: 83048.812 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 24-785 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: BRI1, At4g39400, F23K16.30 / Cell (production host): high five References: UniProt: O22476, receptor protein-tyrosine kinase, non-specific serine/threonine protein kinase #2: Protein | Mass: 21625.393 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 26-221 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: BAK1, ELG, SERK3, At4g33430, F17M5.190 / Cell (production host): high five References: UniProt: Q94F62, receptor protein-tyrosine kinase, non-specific serine/threonine protein kinase |
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-Sugars , 2 types, 7 molecules
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Sugar | |
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-Non-polymers , 2 types, 4 molecules
#5: Chemical | #6: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.88 Å3/Da / Density % sol: 74.8 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 4 Details: 0.1M Citric Acid, 2.0M (NH4)2SO4, pH 4.0, EVAPORATION, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 25, 2013 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→50 Å / Num. all: 45864 / Num. obs: 45084 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Rsym value: 0.061 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RGZ Resolution: 3.602→45.904 Å / SU ML: 0.49 / σ(F): 1.97 / Phase error: 33.88 / 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: 3.602→45.904 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16
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