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- PDB-8if6: Conformational Dynamics of the D53-D3-D14 Complex in Strigolacton... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8if6 | ||||||
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Title | Conformational Dynamics of the D53-D3-D14 Complex in Strigolactone Signaling | ||||||
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![]() | PLANT PROTEIN / D14 D3 D53 SL | ||||||
Function / homology | ![]() 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 / strigolactone biosynthetic process / cuticle development / auxin polar transport / secondary shoot formation ...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 / strigolactone biosynthetic process / cuticle development / auxin polar transport / secondary shoot formation / jasmonic acid mediated signaling pathway / response to water deprivation / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / cullin family protein binding / response to light stimulus / Hydrolases; Acting on ester bonds / hydrolase activity / protein ubiquitination / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.09 Å | ||||||
![]() | Liu, S.M. / Wang, J. | ||||||
Funding support | 1items
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![]() | ![]() Title: Conformational Dynamics of the D53-D3-D14 Complex in Strigolactone Signaling. Authors: Simiao Liu / Jia Wang / Bin Song / Xinqi Gong / Huihui Liu / Qingliang Hu / Junhui Zhang / Qianqian Li / Jie Zheng / Hongwei Wang / H Eric Xu / Jiayang Li / Bing Wang / ![]() Abstract: Strigolactones (SLs) play fundamental roles in regulating plant architecture, which is a major factor determining crop yield. The perception and signal transduction of SLs require the formation of a ...Strigolactones (SLs) play fundamental roles in regulating plant architecture, which is a major factor determining crop yield. The perception and signal transduction of SLs require the formation of a complex containing the receptor DWARF14 (D14), an F-box protein D3 and a transcriptional regulator D53 in an SL-dependent manner. Structural and biochemical analyses of D14 and its orthologs DAD2 and AtD14, D3 and the complexes of ASK1-D3-AtD14 and D3CTH-D14 have made great contributions to understanding the mechanisms of SL perception. However, structural analyses of D53 and the D53-D3-D14 holo-complex are challenging, and the biochemical mechanism underlying the complex assembly remains poorly understood. Here, we found that apo-D53 was rather flexible and reconstituted the holo-complex containing D53, S-phase kinase-associated protein 1 (SKP1), D3 and D14 with rac-GR24. The cryo-electron microscopy (cryo-EM) structure of SKP1-D3-D14 in the presence of D53 was analyzed and superimposed on the crystal structure of ASK1-D3-AtD14 without D53. No large conformational rearrangement was observed, but a 9Å rotation appeared between D14 and AtD14. Using hydrogen-deuterium exchange monitored by mass spectrometry, we analyzed dynamic motifs of D14, D3 and D53 in the D53-SKP1-D3-D14 complex assembly process and further identified two potential interfaces in D53 that are located in the N and D2 domains, respectively. Together, our results uncovered the dynamic conformational changes and built a model of the holo-complex D53-SKP1-D3-D14, offering valuable information for the biochemical and genetic mechanisms of SL perception and signal transduction. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 202.8 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 989 KB | Display | ![]() |
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Full document | ![]() | 1021.3 KB | Display | |
Data in XML | ![]() | 39.6 KB | Display | |
Data in CIF | ![]() | 59 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 35402MC 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: 79308.617 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: D3, Os06g0154200, LOC_Os06g06050, OSJNBa0085L11.6-1 / Production host: ![]() ![]() |
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#2: Protein | Mass: 33545.023 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: D14, D88, HTD2, Os03g0203200, LOC_Os03g10620 / Production host: ![]() ![]() References: UniProt: Q10QA5, Hydrolases; Acting on ester bonds |
#3: Protein | Mass: 19217.693 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: SKP20, OSK20, Os09g0539500, LOC_Os09g36830, B1274F11.9, OsJ_30167 Production host: ![]() ![]() |
-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: Plant protein complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
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: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 700 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
3D reconstruction | Resolution: 7.09 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42499 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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