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- PDB-9ltr: Cryo-EM structure of dimeric DDB1-DDA1-DET1-Ube2e2-COP1 complex -

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Basic information

Entry
Database: PDB / ID: 9ltr
TitleCryo-EM structure of dimeric DDB1-DDA1-DET1-Ube2e2-COP1 complex
Components
  • DET1 homolog
  • DET1- and DDB1-associated protein 1
  • DNA damage-binding protein 1
  • E3 ubiquitin-protein ligase COP1
  • Ubiquitin-conjugating enzyme E2 E2
KeywordsLIGASE / E3 ligase component
Function / homology
Function and homology information


ISG15 transferase activity / ISG15-protein conjugation / negative regulation of fatty acid biosynthetic process / cullin-RING ubiquitin ligase complex / protein K11-linked ubiquitination / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / E2 ubiquitin-conjugating enzyme ...ISG15 transferase activity / ISG15-protein conjugation / negative regulation of fatty acid biosynthetic process / cullin-RING ubiquitin ligase complex / protein K11-linked ubiquitination / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / E2 ubiquitin-conjugating enzyme / biological process involved in interaction with symbiont / response to ionizing radiation / regulation of mitotic cytokinesis / regulation of mitotic cell cycle phase transition / regulation of miRNA-mediated gene silencing / regulation of natural killer cell activation / WD40-repeat domain binding / regulation of cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / regulation of stem cell population maintenance / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin conjugating enzyme activity / ubiquitin ligase complex scaffold activity / negative regulation of adipose tissue development / regulation of cellular response to stress / viral release from host cell / protein monoubiquitination / cullin family protein binding / regulation of DNA-templated DNA replication initiation / protein K63-linked ubiquitination / positive regulation of viral genome replication / positive regulation of gluconeogenesis / positive regulation of G1/S transition of mitotic cell cycle / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / regulation of embryonic development / replication fork processing / proteasomal protein catabolic process / epigenetic regulation of gene expression / nucleotide-excision repair / Autodegradation of the E3 ubiquitin ligase COP1 / regulation of autophagy / Recognition of DNA damage by PCNA-containing replication complex / RING-type E3 ubiquitin transferase / regulation of circadian rhythm / cell population proliferation / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / protein polyubiquitination / Formation of Incision Complex in GG-NER / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / cellular response to UV / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ubiquitin protein ligase activity / rhythmic process / regulation of cell population proliferation / site of double-strand break / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / protein-containing complex assembly / spermatogenesis / ubiquitin-dependent protein catabolic process / damaged DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of apoptotic process / protein-macromolecule adaptor activity / chromosome, telomeric region / nuclear speck / protein ubiquitination / Golgi membrane / ubiquitin protein ligase binding / DNA repair / DNA damage response / nucleolus / protein-containing complex binding / protein-containing complex / DNA binding / : / extracellular exosome / nucleoplasm / zinc ion binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
De-etiolated protein 1, Det1 / De-etiolated protein 1 Det1 / E3 ubiquitin-protein ligase COP1 / DET1- and DDB1-associated protein 1, N-terminal / DET1- and DDB1-associated protein 1 / Det1 complexing ubiquitin ligase / Zinc finger, C3HC4 type (RING finger) / : / Nucleolar protein 10-like, N-terminal domain / : ...De-etiolated protein 1, Det1 / De-etiolated protein 1 Det1 / E3 ubiquitin-protein ligase COP1 / DET1- and DDB1-associated protein 1, N-terminal / DET1- and DDB1-associated protein 1 / Det1 complexing ubiquitin ligase / Zinc finger, C3HC4 type (RING finger) / : / Nucleolar protein 10-like, N-terminal domain / : / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / 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. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
DNA damage-binding protein 1 / DET1 homolog / E3 ubiquitin-protein ligase COP1 / Ubiquitin-conjugating enzyme E2 E2 / DET1- and DDB1-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsSu, M.-Y. / Wang, S. / Teng, F.
Funding support China, 1items
OrganizationGrant numberCountry
Other government2024A1515011683 China
CitationJournal: Nat Commun / Year: 2026
Title: Cryo-EM structure of the human COP1-DET1 ubiquitin ligase complex.
Authors: Shan Wang / Fei Teng / Goran Stjepanovic / Feng Rao / Ming-Yuan Su /
Abstract: Ubiquitin modifications regulate fundamental cellular activities by modulating protein stability and function. The ubiquitin ligase COP1, which is present across species from plants to humans, plays ...Ubiquitin modifications regulate fundamental cellular activities by modulating protein stability and function. The ubiquitin ligase COP1, which is present across species from plants to humans, plays a crucial role in the ubiquitination of developmental transcription factors. While COP1 can function independently, it can also be incorporated into CULLIN4-RING ubiquitin ligase (CRL4) complexes through the DET1 adaptor protein. Despite its biological significance, the structural and functional mechanisms of COP1 and DET1-containing complexes remains poorly understood. Here we present the cryo-electron microscopy structures of human COP1 in complex with DDB1-DDA1-DET1 and Ube2e2, revealing an inactive stacked assembly state. Co-expression with COP1 substrates including c-Jun or ETS2 disrupts this configuration, inducing a conformational rearrangement into a distinct dimeric state that allows substrate access. Structural modelling identifies the spatial organization of COP1 WD40 domains where substrate recruits. DET1 serves as a structural scaffold, bridging COP1 and Ube2e2 to initiate potential ubiquitin addition on substrates, while DDB1 recruits the CULLIN4-RBX1 complex to facilitate Ube2d3-mediated ubiquitin chain elongation. These results reveal the dynamic interplay between the structural states of the CRL4 E3 ligase complex and its substrate specific activation mechanism, offering mechanistic insights into ubiquitination regulation and a basis for future studies on E3 ligase dynamics.
History
DepositionFeb 6, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase COP1
B: DNA damage-binding protein 1
C: E3 ubiquitin-protein ligase COP1
D: DET1 homolog
E: DNA damage-binding protein 1
H: DET1 homolog
I: DET1- and DDB1-associated protein 1
J: Ubiquitin-conjugating enzyme E2 E2
K: Ubiquitin-conjugating enzyme E2 E2
P: DET1- and DDB1-associated protein 1


Theoretical massNumber of molelcules
Total (without water)611,47110
Polymers611,47110
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein E3 ubiquitin-protein ligase COP1 / Constitutive photomorphogenesis protein 1 homolog / hCOP1 / RING finger and WD repeat domain ...Constitutive photomorphogenesis protein 1 homolog / hCOP1 / RING finger and WD repeat domain protein 2 / RING finger protein 200 / RING-type E3 ubiquitin transferase RFWD2


Mass: 80569.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COP1, RFWD2, RNF200 / Production host: Homo sapiens (human)
References: UniProt: Q8NHY2, RING-type E3 ubiquitin transferase
#2: Protein DNA damage-binding protein 1 / DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / ...DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / HBV X-associated protein 1 / XAP-1 / UV-damaged DNA-binding factor / UV-damaged DNA-binding protein 1 / UV-DDB 1 / XPE-binding factor / XPE-BF / Xeroderma pigmentosum group E-complementing protein / XPCe


Mass: 127097.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: Homo sapiens (human) / References: UniProt: Q16531
#3: Protein DET1 homolog / De-etiolated-1 homolog


Mass: 63931.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DET1 / Production host: Homo sapiens (human) / References: UniProt: Q7L5Y6
#4: Protein DET1- and DDB1-associated protein 1 / Placenta cross-immune reaction antigen 1 / PCIA-1


Mass: 11855.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDA1, C19orf58, PCIA1 / Production host: Homo sapiens (human) / References: UniProt: Q9BW61
#5: Protein Ubiquitin-conjugating enzyme E2 E2 / E2 ubiquitin-conjugating enzyme E2 / UbcH8 / Ubiquitin carrier protein E2 / Ubiquitin-protein ligase E2


Mass: 22282.092 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2E2, UBCH8 / Production host: Homo sapiens (human)
References: UniProt: Q96LR5, E2 ubiquitin-conjugating enzyme
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

ComponentName: protein complex of dimeric DDB1-DDA1-DET1-Ube2e2-COP1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.6 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: the purified protein was at 0.535 or 0.3 mg/ml and applied to fresh glow-discharged UltrAuFoil (1.2/1.3, 300 mesh) grids
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 46.55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
Details: The total dose on the specimen was 46.55, 46.32, 47.42, and 48.6 e-/A2, total exposure time of 2.497 or 1.997 sec, fractionated over 50 frames.

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.1_5286model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61817 / Symmetry type: POINT
RefinementHighest resolution: 3.03 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00121109
ELECTRON MICROSCOPYf_angle_d0.33629354
ELECTRON MICROSCOPYf_dihedral_angle_d2.8294243
ELECTRON MICROSCOPYf_chiral_restr0.0454029
ELECTRON MICROSCOPYf_plane_restr0.0014246

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