+Open data
-Basic information
Entry | Database: PDB / ID: 5hyw | |||||||||||||||
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Title | The crystal structure of the D3-ASK1 complex | |||||||||||||||
Components |
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Keywords | SIGNALING PROTEIN/PROTEIN BINDING / F-box protein / SIGNALING PROTEIN-PROTEIN BINDING complex | |||||||||||||||
Function / homology | Function and homology information bud dilation / regulation of shoot system morphogenesis / shoot system morphogenesis / regulation of meristem structural organization / negative regulation of seed germination / positive regulation of response to water deprivation / cuticle development / phragmoplast / auxin polar transport / jasmonic acid mediated signaling pathway ...bud dilation / regulation of shoot system morphogenesis / shoot system morphogenesis / regulation of meristem structural organization / negative regulation of seed germination / positive regulation of response to water deprivation / cuticle development / phragmoplast / auxin polar transport / jasmonic acid mediated signaling pathway / ethylene-activated signaling pathway / response to jasmonic acid / response to auxin / auxin-activated signaling pathway / response to water deprivation / negative regulation of DNA recombination / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / cullin family protein binding / response to light stimulus / chromosome segregation / microtubule cytoskeleton organization / spindle / protein ubiquitination / mitochondrion / nucleus / cytosol Similarity search - Function | |||||||||||||||
Biological species | Oryza sativa subsp. japonica (Japanese rice) Arabidopsis thaliana (thale cress) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å | |||||||||||||||
Authors | Yao, R.F. / Ming, Z.H. / Yan, L.M. / Rao, Z.H. / Lou, Z.Y. / Xie, D.X. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: Nature / Year: 2016 Title: DWARF14 is a non-canonical hormone receptor for strigolactone Authors: Yao, R. / Ming, Z. / Yan, L. / Li, S. / Wang, F. / Ma, S. / Yu, C. / Yang, M. / Chen, L. / Chen, L. / Li, Y. / Yan, C. / Miao, D. / Sun, Z. / Yan, J. / Sun, Y. / Wang, L. / Chu, J. / Fan, S. ...Authors: Yao, R. / Ming, Z. / Yan, L. / Li, S. / Wang, F. / Ma, S. / Yu, C. / Yang, M. / Chen, L. / Chen, L. / Li, Y. / Yan, C. / Miao, D. / Sun, Z. / Yan, J. / Sun, Y. / Wang, L. / Chu, J. / Fan, S. / He, W. / Deng, H. / Nan, F. / Li, J. / Rao, Z. / Lou, Z. / Xie, D. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hyw.cif.gz | 271.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hyw.ent.gz | 211.8 KB | Display | PDB format |
PDBx/mmJSON format | 5hyw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hyw_validation.pdf.gz | 476.5 KB | Display | wwPDB validaton report |
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Full document | 5hyw_full_validation.pdf.gz | 513.9 KB | Display | |
Data in XML | 5hyw_validation.xml.gz | 48.1 KB | Display | |
Data in CIF | 5hyw_validation.cif.gz | 65.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hy/5hyw ftp://data.pdbj.org/pub/pdb/validation_reports/hy/5hyw | HTTPS FTP |
-Related structure data
Related structure data | 5hzgSC 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 81153.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice) Gene: D3, Os06g0154200, LOC_Os06g06050, OSJNBa0085L11.6-1 Production host: Insect cell expression vector pTIE1 (others) References: UniProt: Q5VMP0 #2: Protein | Mass: 19004.215 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SKP1A, ASK1, SKP1, UIP1, At1g75950, T4O12.17 Production host: Insect cell expression vector pTIE1 (others) References: UniProt: Q39255 |
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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: 2.57 Å3/Da / Density % sol: 52.12 % |
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Crystal grow | Temperature: 291 K / Method: evaporation / pH: 6.5 Details: 0.2M Lithium sulfate monohydrate, 0.1M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3→81.89 Å / Num. obs: 38298 / % possible obs: 94.1 % / Redundancy: 3.69 % / Net I/σ(I): 12 |
Reflection shell | Resolution: 3→3.05 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5HZG Resolution: 3.01→81.89 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.814 / SU B: 22.917 / SU ML: 0.419 / Cross valid method: THROUGHOUT / ESU R Free: 0.587 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.428 Å2
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Refinement step | Cycle: LAST / Resolution: 3.01→81.89 Å
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Refine LS restraints |
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