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- EMDB-31968: Cryo-EM structure of Ultraviolet-B activated UVR8 in complex with COP1 -

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Basic information

Entry
Database: EMDB / ID: EMD-31968
TitleCryo-EM structure of Ultraviolet-B activated UVR8 in complex with COP1
Map data
Sample
  • Complex: UVR8-COP1 complex
    • Complex: COP1
      • Protein or peptide: E3 ubiquitin-protein ligase COP1
    • Complex: UVR8
      • Protein or peptide: Ultraviolet-B receptor UVR8
KeywordsCOP1 / UVR8 / SIGNALING PROTEIN
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 / nuclear body / protein ubiquitination / DNA repair / chromatin binding / chromatin / protein homodimerization activity / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase COP1 / : / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Zinc finger, C3HC4 type (RING finger) / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. ...E3 ubiquitin-protein ligase COP1 / : / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Zinc finger, C3HC4 type (RING finger) / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / 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. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase COP1 / Ultraviolet-B receptor UVR8
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsWang YD / Wang LX
Funding support China, 1 items
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, 2021-
Header (metadata) releaseMay 4, 2022-
Map releaseMay 4, 2022-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31968.png

Downloads & links

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Map

FileDownload / File: emd_31968.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 280 pix.
= 231.56 Å		0.83 Å/pix.
x 280 pix.
= 231.56 Å		0.83 Å/pix.
x 280 pix.
= 231.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.827 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-1.7555337 - 2.8597758
Average (Standard dev.)-0.00018679631 (±0.052545037)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 231.56001 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : UVR8-COP1 complex

EntireName: UVR8-COP1 complex
Components
  • Complex: UVR8-COP1 complex
    • Complex: COP1
      • Protein or peptide: E3 ubiquitin-protein ligase COP1
    • Complex: UVR8
      • Protein or peptide: Ultraviolet-B receptor UVR8

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Supramolecule #1: UVR8-COP1 complex

SupramoleculeName: UVR8-COP1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Supramolecule #2: COP1

SupramoleculeName: COP1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Supramolecule #3: UVR8

SupramoleculeName: UVR8 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2

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Macromolecule #1: E3 ubiquitin-protein ligase COP1

MacromoleculeName: E3 ubiquitin-protein ligase COP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 79.731203 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKG DYKDDDDKID YKDDDDKGSM EEISTDPVVP AVKPDPRTSS VGEGANRHEN DDGGSGGSEI GAPDLDKDLL CPICMQIIK DAFLTACGHS FCYMCIITHL RNKSDCPCCS QHLTNNQLYP NFLLDKLLKK TSARHVSKTA SPLDQFREAL Q RGCDVSIK ...String:
MDYKDDDDKG DYKDDDDKID YKDDDDKGSM EEISTDPVVP AVKPDPRTSS VGEGANRHEN DDGGSGGSEI GAPDLDKDLL CPICMQIIK DAFLTACGHS FCYMCIITHL RNKSDCPCCS QHLTNNQLYP NFLLDKLLKK TSARHVSKTA SPLDQFREAL Q RGCDVSIK EVDNLLTLLA ERKRKMEQEE AERNMQILLD FLHCLRKQKV DELNEVQTDL QYIKEDINAV ERHRIDLYRA RD RYSVKLR MLGDDPSTRN AWPHEKNQIG FNSNSLSIRG GNFVGNYQNK KVEGKAQGSS HGLPKKDALS GSDSQSLNQS TVS MARKKR IHAQFNDLQE CYLQKRRQLA DQPNSKQEND KSVVRREGYS NGLADFQSVL TTFTRYSRLR VIAEIRHGDI FHSA NIVSS IEFDRDDELF ATAGVSRCIK VFDFSSVVNE PADMQCPIVE MSTRSKLSCL SWNKHEKNHI ASSDYEGIVT VWDVT TRQS LMEYEEHEKR AWSVDFSRTE PSMLVSGSDD CKVKVWCTRQ EASVINIDMK ANICCVKYNP GSSNYIAVGS ADHHIH YYD LRNISQPLHV FSGHKKAVSY VKFLSNNELA SASTDSTLRL WDVKDNLPVR TFRGHTNEKN FVGLTVNSEY LACGSET NE VYVYHKEITR PVTSHRFGSP DMDDAEEEAG SYFISAVCWK SDSPTMLTAN SQGTIKVLVL AA

UniProtKB: E3 ubiquitin-protein ligase COP1

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Macromolecule #2: Ultraviolet-B receptor UVR8

MacromoleculeName: Ultraviolet-B receptor UVR8 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 50.226488 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH SDEVDAHMMA EDMAADEVTA PPRKVLIISA GASHSVALLS GDIVCSWGRG EDGQLGHGDA EDRPSPTQL SALDGHQIVS VTCGADHTVA YSQSGMEVYS WGWGDFGRLG HGNSSDLFTP LPIKALHGIR IKQIACGDSH C LAVTMEGE ...String:
MGSSHHHHHH SSGLVPRGSH SDEVDAHMMA EDMAADEVTA PPRKVLIISA GASHSVALLS GDIVCSWGRG EDGQLGHGDA EDRPSPTQL SALDGHQIVS VTCGADHTVA YSQSGMEVYS WGWGDFGRLG HGNSSDLFTP LPIKALHGIR IKQIACGDSH C LAVTMEGE VQSWGRNQNG QLGLGDTEDS LVPQKIQAFE GIRIKMVAAG AEHTAAVTED GDLYGWGWGR YGNLGLGDRT DR LVPERVT STGGEKMSMV ACGWRHTISV SYSGALYTYG WSKYGQLGHG DLEDHLIPHK LEALSNSFIS QISGGWRHTM ALT SDGKLY GWGWNKFGQV GVGNNLDQCS PVQVRFPDDQ KVVQVSCGWR HTLAVTERNN VFAWGRGTNG QLGIGESVDR NFPK IIEAL SVDGASGQHI ESSNIDPSSG KSWVSPAERY AVVPDETGLT DGSSKGNGGD ISVPQTDVKR VRI

UniProtKB: Ultraviolet-B receptor UVR8

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.55 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: RANDOM CONICAL TILT
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 170284
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD

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