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- PDB-7vgg: Cryo-EM structure of Ultraviolet-B activated UVR8 in complex with COP1 -

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Basic information

Entry
Database: PDB / ID: 7vgg
TitleCryo-EM structure of Ultraviolet-B activated UVR8 in complex with COP1
Components
  • E3 ubiquitin-protein ligase COP1
  • Ultraviolet-B receptor UVR8
KeywordsSIGNALING PROTEIN / COP1 / UVR8
Function / homology
Function and homology information


skotomorphogenesis / anthocyanin-containing compound metabolic process / shade avoidance / positive regulation of flavonoid biosynthetic process / photoperiodism, flowering / red, far-red light phototransduction / regulation of stomatal movement / photomorphogenesis / nuclear ubiquitin ligase complex / entrainment of circadian clock ...skotomorphogenesis / anthocyanin-containing compound metabolic process / shade avoidance / positive regulation of flavonoid biosynthetic process / photoperiodism, flowering / red, far-red light phototransduction / regulation of stomatal movement / photomorphogenesis / nuclear ubiquitin ligase complex / entrainment of circadian clock / response to UV-B / plastid / Cul4-RING E3 ubiquitin ligase complex / photoreceptor activity / response to UV / guanyl-nucleotide exchange factor activity / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / nuclear body / protein ubiquitination / DNA repair / chromatin binding / chromatin / protein homodimerization activity / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase COP1 / : / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / RCC1-like domain / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Zinc finger, C3HC4 type (RING finger) ...E3 ubiquitin-protein ligase COP1 / : / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / RCC1-like domain / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / 7 Propeller / Methylamine Dehydrogenase; Chain H / Zinc finger RING-type profile. / Zinc finger, RING-type / WD domain, G-beta repeat / Zinc finger, RING/FYVE/PHD-type / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase COP1 / Ultraviolet-B receptor UVR8
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsWang, Y.D. / Wang, L.X. / Guan, Z.Y. / Yin, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2018YFA0507700 China
CitationJournal: 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
DepositionSep 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.0May 4, 2022Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 4, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 4, 2022Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0May 4, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 4, 2022Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
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Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3Jun 18, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase COP1
B: Ultraviolet-B receptor UVR8


Theoretical massNumber of molelcules
Total (without water)129,9582
Polymers129,9582
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2800 Å2
ΔGint1 kcal/mol
Surface area24240 Å2

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Components

#1: Protein E3 ubiquitin-protein ligase COP1 / Constitutive photomorphogenesis protein 1 / RING-type E3 ubiquitin transferase COP1


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
#2: Protein Ultraviolet-B receptor UVR8 / Protein UV-B RESISTANCE 8 / RCC1 domain-containing protein UVR8


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
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1UVR8-COP1 complexCOMPLEXall0MULTIPLE SOURCES
2COP1COMPLEX#11RECOMBINANT
3UVR8COMPLEX#21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Arabidopsis thaliana (thale cress)3702
32Arabidopsis thaliana (thale cress)3702
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
11Homo sapien (human)9606HEK293
22Escherichia coli BL21(DE3) (bacteria)469008
Buffer solutionpH: 7.5
SpecimenConc.: 0.55 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.1_4122: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 170284 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0045394
ELECTRON MICROSCOPYf_angle_d0.4847311
ELECTRON MICROSCOPYf_dihedral_angle_d4.377733
ELECTRON MICROSCOPYf_chiral_restr0.046793
ELECTRON MICROSCOPYf_plane_restr0.003944

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