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- PDB-9oi8: Cryo-EM Structure of the Arabidopsis GA3-GID1A-RGA-SLY1-ASK1 Comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9oi8 | ||||||
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Title | Cryo-EM Structure of the Arabidopsis GA3-GID1A-RGA-SLY1-ASK1 Complex (Alternative Conformation) | ||||||
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![]() | PLANT PROTEIN / RGA / DELLA / GID1 / SLY1 / ASK1 / GA | ||||||
Function / homology | ![]() regulation of gibberellic acid mediated signaling pathway / fruit morphogenesis / gibberellin mediated signaling pathway / positive regulation of gibberellic acid mediated signaling pathway / floral organ morphogenesis / negative regulation of trichome patterning / negative regulation of developmental vegetative growth / negative regulation of leaf development / regulation of seed dormancy process / gibberellin binding ...regulation of gibberellic acid mediated signaling pathway / fruit morphogenesis / gibberellin mediated signaling pathway / positive regulation of gibberellic acid mediated signaling pathway / floral organ morphogenesis / negative regulation of trichome patterning / negative regulation of developmental vegetative growth / negative regulation of leaf development / regulation of seed dormancy process / gibberellin binding / seed dormancy process / negative regulation of gibberellic acid mediated signaling pathway / positive regulation of fertilization / meiotic cytokinesis / response to gibberellin / gibberellic acid mediated signaling pathway / phragmoplast / jasmonic acid mediated signaling pathway / regulation of seed germination / seed germination / ethylene-activated signaling pathway / response to far red light / response to jasmonic acid / Hydrolases / response to auxin / auxin-activated signaling pathway / negative regulation of DNA recombination / SCF ubiquitin ligase complex / regulation of protein catabolic process / response to cold / chromosome segregation / promoter-specific chromatin binding / microtubule cytoskeleton organization / spindle / ubiquitin-dependent protein catabolic process / cellular response to hypoxia / hydrolase activity / transcription cis-regulatory region binding / protein ubiquitination / DNA-binding transcription factor activity / positive regulation of gene expression / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / mitochondrion / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.81 Å | ||||||
![]() | Dahal, P. / Sharma, K. / Borgnia, M. / Zhou, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Insights into Proteolysis-Dependent and -Independent Suppression of the Master Regulator DELLA by Gibberellin Receptor Authors: Dahal, P. / Wang, Y. / Hu, J. / Park, J. / Forker, K. / Zhang, Z. / Sharma, K. / Borgnia, M. / Sun, T.P. / Zhou, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 210.1 KB | Display | ![]() |
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PDB format | ![]() | 159 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 45.8 KB | Display | |
Data in CIF | ![]() | 68.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 70510MC ![]() 9o4jC ![]() 9o4kC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 65253.309 Da / Num. of mol.: 1 / Mutation: K163Q-R164Q-K166Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 39775.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 21069.963 Da / Num. of mol.: 1 / Mutation: E138K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#4: Protein | Mass: 21273.586 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#5: Chemical | ChemComp-GA3 / |
Has ligand of interest | N |
Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: GA3-GID1A-RGA-SLY1-ASK1 Complex / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.21.2_5419 / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 556557 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS) | ||||||||||||||||||||||||
Refine LS restraints |
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