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Yorodumi- PDB-7vgg: Cryo-EM structure of Ultraviolet-B activated UVR8 in complex with COP1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vgg | ||||||
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Title | Cryo-EM structure of Ultraviolet-B activated UVR8 in complex with COP1 | ||||||
Components |
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Keywords | SIGNALING PROTEIN / COP1 / UVR8 | ||||||
Function / homology | Function and homology information anthocyanin-containing compound metabolic process / shade avoidance / positive regulation of flavonoid biosynthetic process / skotomorphogenesis / photoperiodism, flowering / red, far-red light phototransduction / photomorphogenesis / regulation of stomatal movement / nuclear ubiquitin ligase complex / entrainment of circadian clock ...anthocyanin-containing compound metabolic process / shade avoidance / positive regulation of flavonoid biosynthetic process / skotomorphogenesis / photoperiodism, flowering / red, far-red light phototransduction / photomorphogenesis / regulation of stomatal movement / nuclear ubiquitin ligase complex / entrainment of circadian clock / Cul4-RING E3 ubiquitin ligase complex / response to UV-B / plastid / photoreceptor activity / response to UV / guanyl-nucleotide exchange factor activity / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / protein ubiquitination / nuclear body / DNA repair / chromatin binding / chromatin / protein homodimerization activity / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
Authors | Wang, Y.D. / Wang, L.X. / Guan, Z.Y. / Yin, P. | ||||||
Funding support | China, 1items
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Citation | Journal: Sci Adv / Year: 2022 Title: Structural insight into UV-B-activated UVR8 bound to COP1. Authors: Yidong Wang / Lixia Wang / Zeyuan Guan / Hongfei Chang / Ling Ma / Cuicui Shen / Liang Qiu / Junjie Yan / Delin Zhang / Jian Li / Xing Wang Deng / Ping Yin / Abstract: The CONSTITUTIVE PHOTOMORPHOGENIC 1-SUPPRESSOR OF PHYA-105 (COP1-SPA) complex is a central repressor of photomorphogenesis. This complex acts as an E3 ubiquitin ligase downstream of various light ...The CONSTITUTIVE PHOTOMORPHOGENIC 1-SUPPRESSOR OF PHYA-105 (COP1-SPA) complex is a central repressor of photomorphogenesis. This complex acts as an E3 ubiquitin ligase downstream of various light signaling transduced from multiple photoreceptors in plants. How the COP1-SPA activity is regulated by divergent light-signaling pathways remains largely elusive. Here, we reproduced the regulation pathway of COP1-SPA in ultraviolet-B (UV-B) signaling in vitro and determined the cryo-electron microscopy structure of UV-B receptor UVR8 in complex with COP1. The complex formation is mediated by two-interface interactions between UV-B-activated UVR8 and COP1. Both interfaces are essential for the competitive binding of UVR8 against the signaling hub component HY5 to the COP1-SPA complex. We also show that RUP2 dissociates UVR8 from the COP1-SPA4-UVR8 complex and facilitates its redimerization. Our results support a UV-B signaling model that the COP1-SPA activity is repressed by UV-B-activated UVR8 and derepressed by RUP2, owing to competitive binding, and provide a framework for studying the regulatory roles of distinct photoreceptors on photomorphogenesis. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vgg.cif.gz | 135.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vgg.ent.gz | 102.3 KB | Display | PDB format |
PDBx/mmJSON format | 7vgg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vg/7vgg ftp://data.pdbj.org/pub/pdb/validation_reports/vg/7vgg | HTTPS FTP |
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-Related structure data
Related structure data | 31968MC M: map data used to model this data C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 79731.203 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: COP1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) References: UniProt: P43254, RING-type E3 ubiquitin transferase |
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#2: Protein | Mass: 50226.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: UVR8 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9FN03 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Conc.: 0.55 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.1_4122: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 170284 / Symmetry type: POINT | ||||||||||||||||||||||||
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