+Open data
-Basic information
Entry | Database: PDB / ID: 7sa1 | ||||||
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Title | LRR-F-Box plant ubiquitin ligase | ||||||
Components |
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Keywords | SIGNALING PROTEIN / rice D3 / ASK1 / E3-Ub ligase | ||||||
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 | Arabidopsis thaliana (thale cress) Oryza sativa subsp. japonica (Japanese rice) Oryza sativa tropical japonica subgroup (rice) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å | ||||||
Authors | Palayam, M. / Shabek, N. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat.Plants / Year: 2022 Title: A conformational switch in the SCF-D3/MAX2 ubiquitin ligase facilitates strigolactone signalling. Authors: Tal, L. / Palayam, M. / Ron, M. / Young, A. / Britt, A. / Shabek, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sa1.cif.gz | 303.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sa1.ent.gz | 240.4 KB | Display | PDB format |
PDBx/mmJSON format | 7sa1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7sa1_validation.pdf.gz | 489 KB | Display | wwPDB validaton report |
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Full document | 7sa1_full_validation.pdf.gz | 507.2 KB | Display | |
Data in XML | 7sa1_validation.xml.gz | 51.6 KB | Display | |
Data in CIF | 7sa1_validation.cif.gz | 69.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sa/7sa1 ftp://data.pdbj.org/pub/pdb/validation_reports/sa/7sa1 | HTTPS FTP |
-Related structure data
Related structure data | 6brpS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 17876.043 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: Baculovirus expression vector pFastBac1-HM / References: UniProt: Q39255 #2: Protein | Mass: 75843.016 Da / Num. of mol.: 2 / Mutation: D720K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice), (gene. exp.) Oryza sativa tropical japonica subgroup (rice) Gene: D3, Os06g0154200, LOC_Os06g06050, OSJNBa0085L11.6-1, D3 Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: Q5VMP0 #3: Chemical | ChemComp-PEG / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | Sequence details | Non-conserved disordered loop residues 478-515 have been eliminated for crystallization purposes by ...Non-conserved disordered loop residues 478-515 have been eliminated for crystallization purposes by introducing TEV cleavage (NLYFQS), creating fragments 1 to 477 and 516 to 720 that assembled together during purification. | |
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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: 2.92 Å3/Da / Density % sol: 57.82 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 0.1M Ammonium acetate, 0.1M Sodium formate, 0.1M Sodium citrate tribasic dihydrate, 0.1M Potassium sodium tartrate tetrahydrate, 0.1M Sodium oxamate, 0.1M Tris, 0.1M Bicine and 30% PEG 500 ...Details: 0.1M Ammonium acetate, 0.1M Sodium formate, 0.1M Sodium citrate tribasic dihydrate, 0.1M Potassium sodium tartrate tetrahydrate, 0.1M Sodium oxamate, 0.1M Tris, 0.1M Bicine and 30% PEG 500 MME and PEG 20000 at pH 8.5. PH range: 5.0-6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.21→48.9 Å / Num. obs: 34685 / % possible obs: 97.59 % / Redundancy: 3 % / Rsym value: 0.089 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 3.21→3.32 Å / Num. unique obs: 3119 / Rsym value: 0.715 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6BRP Resolution: 3.21→48.9 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.3 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 169.19 Å2 / Biso mean: 45.172 Å2 / Biso min: 1.04 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.21→48.9 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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