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- EMDB-44638: Structure of the human DDD-Ube2e2 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-44638
TitleStructure of the human DDD-Ube2e2 complex
Map data
Sample
  • Complex: Complex of DDB1(deltaBPB)-DET1-DDA1-Ube2e2
    • Complex: DDD Complex
      • Protein or peptide: DNA damage-binding protein 1
      • Protein or peptide: DET1 homolog
      • Protein or peptide: DET1- and DDB1-associated protein 1
    • Complex: Ube2e2
      • Protein or peptide: Ubiquitin-conjugating enzyme E2 E2
KeywordsDDB1 / DDA1 / DET1 / DCAF / ubiquitin conjugating enzyme / PROTEIN BINDING
Function / homology
Function and homology information


ISG15 transferase activity / ISG15-protein conjugation / cullin-RING ubiquitin ligase complex / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / protein K11-linked ubiquitination / UV-damage excision repair / biological process involved in interaction with symbiont ...ISG15 transferase activity / ISG15-protein conjugation / cullin-RING ubiquitin ligase complex / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / protein K11-linked ubiquitination / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / E2 ubiquitin-conjugating enzyme / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / ubiquitin conjugating enzyme activity / cullin family protein binding / viral release from host cell / protein K63-linked ubiquitination / protein monoubiquitination / positive regulation of G1/S transition of mitotic cell cycle / ectopic germ cell programmed cell death / ubiquitin-like ligase-substrate adaptor activity / positive regulation of viral genome replication / protein K48-linked ubiquitination / proteasomal protein catabolic process / positive regulation of gluconeogenesis / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / regulation of circadian rhythm / Wnt signaling pathway / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / protein polyubiquitination / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / cellular response to UV / rhythmic process / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / site of double-strand break / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / chromosome, telomeric region / protein ubiquitination / DNA repair / apoptotic process / ubiquitin protein ligase binding / DNA damage response / protein-containing complex binding / negative regulation of apoptotic process / nucleolus / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
De-etiolated protein 1, Det1 / De-etiolated protein 1 Det1 / DET1- and DDB1-associated protein 1, N-terminal / DET1- and DDB1-associated protein 1 / Det1 complexing ubiquitin ligase / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / RSE1/DDB1/CPSF1 first beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / : / CPSF A subunit region ...De-etiolated protein 1, Det1 / De-etiolated protein 1 Det1 / DET1- and DDB1-associated protein 1, N-terminal / DET1- and DDB1-associated protein 1 / Det1 complexing ubiquitin ligase / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / RSE1/DDB1/CPSF1 first beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / : / CPSF A subunit region / 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 / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
DNA damage-binding protein 1 / DET1 homolog / Ubiquitin-conjugating enzyme E2 E2 / DET1- and DDB1-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsLoughran T / Turk LS / Brown SHJ / Mace PD
Funding support New Zealand, 1 items
OrganizationGrant numberCountry
Marsden FundUOO2102 New Zealand
CitationJournal: Sci Adv / Year: 2025
Title: DET1 dynamics underlie cooperative ubiquitination by CRL4 complexes.
Authors: Abigail E Burgess / Tarren A Loughran / Liam S Turk / Hunter G Nyvall / Jessica L Dunlop / Sam A Jamieson / Jack R Curry / John E Burke / Pavel Filipcik / Simon H J Brown / Peter D Mace /
Abstract: Transcription factor ubiquitination is a decisive regulator of growth and development. The DET1-DDB1-DDA1 (DDD) complex associates with the Cullin-4 ubiquitin ligase (CRL4) and a second ubiquitin ...Transcription factor ubiquitination is a decisive regulator of growth and development. The DET1-DDB1-DDA1 (DDD) complex associates with the Cullin-4 ubiquitin ligase (CRL4) and a second ubiquitin ligase, COP1, to control ubiquitination of transcription factors involved in neurological, metabolic, and immune cell development. Here, we report the structure of the human DDD complex, revealing a specific segment of DET1 that can recruit ubiquitin-conjugating (E2) enzymes. Structural variability analysis, mass spectrometry, and mutagenesis based on AlphaFold predictions suggest that dynamic closure of DET1, stabilized by DDA1, underlies coordinated recruitment of E2 enzymes and COP1. Biochemical assays suggest that the E2 acts as a recruitment factor to bring COP1 to DET1 for more effective substrate ubiquitination, which parallels a catalytically inactive E2 enzyme (COP10) in plant DDD complexes. This work provides a clear architecture for regulation and cooperative CRL4 complex assembly, which can affect degradation of diverse targets by COP1 complexes.
History
DepositionApr 26, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44638.png

Downloads & links

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Map

FileDownload / File: emd_44638.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 384 pix.
= 249.6 Å		0.65 Å/pix.
x 384 pix.
= 249.6 Å		0.65 Å/pix.
x 384 pix.
= 249.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00817
Minimum - Maximum-0.054935984 - 0.1051255
Average (Standard dev.)0.00004724485 (±0.0028136796)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 249.59999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_44638_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_44638_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Complex of DDB1(deltaBPB)-DET1-DDA1-Ube2e2

EntireName: Complex of DDB1(deltaBPB)-DET1-DDA1-Ube2e2
Components
  • Complex: Complex of DDB1(deltaBPB)-DET1-DDA1-Ube2e2
    • Complex: DDD Complex
      • Protein or peptide: DNA damage-binding protein 1
      • Protein or peptide: DET1 homolog
      • Protein or peptide: DET1- and DDB1-associated protein 1
    • Complex: Ube2e2
      • Protein or peptide: Ubiquitin-conjugating enzyme E2 E2

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Supramolecule #1: Complex of DDB1(deltaBPB)-DET1-DDA1-Ube2e2

SupramoleculeName: Complex of DDB1(deltaBPB)-DET1-DDA1-Ube2e2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: DDD Complex

SupramoleculeName: DDD Complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Ube2e2

SupramoleculeName: Ube2e2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DNA damage-binding protein 1

MacromoleculeName: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 95.337336 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAHHHHHHSA ALEVLFQMSY NYVVTAQKPT AVNGCVTGHF TSAEDLNLLI AKNTRLEIYV VTAEGLRPVK EVGMYGKIAV MELFRPKGE SKDLLFILTA KYNACILEYK QSGESIDIIT RAHGNVQDRI GRPSETGIIG IIDPECRMIG LRLYDGLFKV I PLDRDNKE ...String:
MAHHHHHHSA ALEVLFQMSY NYVVTAQKPT AVNGCVTGHF TSAEDLNLLI AKNTRLEIYV VTAEGLRPVK EVGMYGKIAV MELFRPKGE SKDLLFILTA KYNACILEYK QSGESIDIIT RAHGNVQDRI GRPSETGIIG IIDPECRMIG LRLYDGLFKV I PLDRDNKE LKAFNIRLEE LHVIDVKFLY GCQAPTICFV YQDPQGRHVK TYEVSLREKE FNKGPWKQEN VEAEASMVIA VP EPFGGAI IIGQESITYH NGDKYLAIAP PIIKQSTIVC HNRVDPNGSR YLLGDMEGRL FMLLLEKEEQ MDGTVTLKDL RVE LLGETS IAECLTYLDN GVVFVGSRLG DSQLVKLNVD SNEQGSYVVA METFTNLGPI VDMCVVDLER QGQGQLVTCS GAFK EGSLR IIRNGIGGNG NSGEIQKLHI RTVPLYESPR KICYQEVSQC FGVLSSRIEV QDTSGGTTAL RPSASTQALS SSVSS SKLF SSSTAPHETS FGEEVEVHNL LIIDQHTFEV LHAHQFLQNE YALSLVSCKL GKDPNTYFIV GTAMVYPEEA EPKQGR IVV FQYSDGKLQT VAEKEVKGAV YSMVEFNGKL LASINSTVRL YEWTTEKELR TECNHYNNIM ALYLKTKGDF ILVGDLM RS VLLLAYKPME GNFEEIARDF NPNWMSAVEI LDDDNFLGAE NAFNLFVCQK DSAATTDEER QHLQEVGLFH LGEFVNVF C HGSLVMQNLG ETSTPTQGSV LFGTVNGMIG LVTSLSESWY NLLLDMQNRL NKVIKSVGKI EHSFWRSFHT ERKTEPATG FIDGDLIESF LDISRPKMQE VVANLQYDDG SGMKREATAD DLIKVVEELT RIH

UniProtKB: DNA damage-binding protein 1, DNA damage-binding protein 1

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Macromolecule #2: DET1 homolog

MacromoleculeName: DET1 homolog / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 67.903617 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KLEVLFQGPG DHHVSTIKPR RIQNQNVIHR LERRRISSGK AGTHWHQVRV FHQNVFPNF TVVNVEKPPC FLRKFSPDGR YFIAFSSDQT SLEIYEYQGC QAAEDLLQGY EGEILSNGND QRSVNIRGRL F ERFFVLLH ...String:
MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KLEVLFQGPG DHHVSTIKPR RIQNQNVIHR LERRRISSGK AGTHWHQVRV FHQNVFPNF TVVNVEKPPC FLRKFSPDGR YFIAFSSDQT SLEIYEYQGC QAAEDLLQGY EGEILSNGND QRSVNIRGRL F ERFFVLLH ITNVAANGEH LNRECSLFTD DCRCVIVGSA AYLPDEPHPP FFEVYRNSES VTPNPRSPLE DYSLHIIDLH TG RLCDTRT FKCDKVVLSH NQGLYLYKNI LAILSVQQQT IHVFQVTPEG TFIDVRTIGR FCYEDDLLTV SAVFPEVQRD SQT GMANPF RDPFINSLKH RLLVYLWRRA EQDGSAMAKR RFFQYFDQLR QLRMWKMQLL DENHLFIKYT SEDVVTLRVT DPSQ ASFFV VYNMVTTEVI AVFENTSDEL LELFENFCDL FRNATLHSEV QFPCSASSNN FARQIQRRFK DTIINAKYGG HTEAV RRLL GQLPISAQSY SGSPYLDLSL FSYDDKWVSV MERPKTCGDH PIRFYARDSG LLKFEIQAGL LGRPINHTVR RLVAFT FHP FEPFAISVQR TNAEYVVNFH MRHCCT

UniProtKB: DET1 homolog

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Macromolecule #3: DET1- and DDB1-associated protein 1

MacromoleculeName: DET1- and DDB1-associated protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.855297 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MADFLKGLPV YNKSNFSRFH ADSVCKASNR RPSVYLPTRE YPSEQIIVTE KTNILLRYLH QQWDKKNAAK KRDQEQVELE GESSAPPRK VARTDSPDMH EDT

UniProtKB: DET1- and DDB1-associated protein 1

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Macromolecule #4: Ubiquitin-conjugating enzyme E2 E2

MacromoleculeName: Ubiquitin-conjugating enzyme E2 E2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: E2 ubiquitin-conjugating enzyme
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.352371 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAHHHHHHSA ALEVLFQGPG STEAQRVDDS PSTSGGSSDG DQRESVQQEP EREQVQPKKK EGKISSKTAA KLSTSAKRIQ KELAEITLD PPPNCSAGPK GDNIYEWRST ILGPPGSVYE GGVFFLDITF SPDYPFKPPK VTFRTRIYHC NINSQGVICL D ILKDNWSP ...String:
MAHHHHHHSA ALEVLFQGPG STEAQRVDDS PSTSGGSSDG DQRESVQQEP EREQVQPKKK EGKISSKTAA KLSTSAKRIQ KELAEITLD PPPNCSAGPK GDNIYEWRST ILGPPGSVYE GGVFFLDITF SPDYPFKPPK VTFRTRIYHC NINSQGVICL D ILKDNWSP ALTISKVLLS ICSLLTDCNP ADPLVGSIAT QYMTNRAEHD RMARQWTKRY AT

UniProtKB: Ubiquitin-conjugating enzyme E2 E2

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 61234
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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