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- EMDB-63372: Cryo-EM structure of DDB1-DDA1-DET1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-63372
TitleCryo-EM structure of DDB1-DDA1-DET1 complex
Map datafull map
Sample
  • Complex: protein complex of DDB1-DDA1-DET1 complex
    • Protein or peptide: DET1 homolog
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: DET1- and DDB1-associated protein 1
KeywordsE3 ligase component / LIGASE
Function / homology
Function and homology information


cullin-RING ubiquitin ligase complex / 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 / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex ...cullin-RING ubiquitin ligase complex / 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 / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / viral release from host cell / cullin family protein binding / ectopic germ cell programmed cell death / positive regulation of viral genome replication / ubiquitin-like ligase-substrate adaptor activity / proteasomal protein catabolic process / positive regulation of gluconeogenesis / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / regulation of circadian rhythm / 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 / Formation of Incision Complex in GG-NER / Wnt signaling pathway / protein polyubiquitination / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / site of double-strand break / Neddylation / protein-containing complex assembly / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / chromosome, telomeric region / protein ubiquitination / DNA repair / apoptotic process / DNA damage response / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein-containing complex binding / nucleolus / protein-containing complex / extracellular space / DNA binding / extracellular exosome / nucleoplasm / 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 / 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 ...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 / 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 / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
DNA damage-binding protein 1 / DET1 homolog / DET1- and DDB1-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsSu M-Y / Wang S / Teng F
Funding support China, 1 items
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, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63372.png

Downloads & links

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Map

FileDownload / File: emd_63372.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0938
Minimum - Maximum-0.62889886 - 1.3126065
Average (Standard dev.)-0.0014008244 (±0.031841747)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: deepemhancer post-processing map

Fileemd_63372_additional_1.map
Annotationdeepemhancer post-processing map
Projections & Slices
AxesZYX

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Half map: half map - B

Fileemd_63372_half_map_1.map
Annotationhalf map - B
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: half map - A

Fileemd_63372_half_map_2.map
Annotationhalf map - A
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Sample components

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Entire : protein complex of DDB1-DDA1-DET1 complex

EntireName: protein complex of DDB1-DDA1-DET1 complex
Components
  • Complex: protein complex of DDB1-DDA1-DET1 complex
    • Protein or peptide: DET1 homolog
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: DET1- and DDB1-associated protein 1

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Supramolecule #1: protein complex of DDB1-DDA1-DET1 complex

SupramoleculeName: protein complex of DDB1-DDA1-DET1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 200 KDa

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Macromolecule #1: DET1 homolog

MacromoleculeName: DET1 homolog / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 63.931367 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDHHVSTIKP RRIQNQNVIH RLERRRISSG KAGTHWHQVR VFHQNVFPNF TVVNVEKPPC FLRKFSPDGR YFIAFSSDQT SLEIYEYQG CQAAEDLLQG YEGEILSNGN DQRSVNIRGR LFERFFVLLH ITNVAANGEH LNRECSLFTD DCRCVIVGSA A YLPDEPHP ...String:
MDHHVSTIKP RRIQNQNVIH RLERRRISSG KAGTHWHQVR VFHQNVFPNF TVVNVEKPPC FLRKFSPDGR YFIAFSSDQT SLEIYEYQG CQAAEDLLQG YEGEILSNGN DQRSVNIRGR LFERFFVLLH ITNVAANGEH LNRECSLFTD DCRCVIVGSA A YLPDEPHP PFFEVYRNSE SVTPNPRSPL EDYSLHIIDL HTGRLCDTRT FKCDKVVLSH NQGLYLYKNI LAILSVQQQT IH VFQVTPE GTFIDVRTIG RFCYEDDLLT VSAVFPEVQR DSQTGMANPF RDPFINSLKH RLLVYLWRRA EQDGSAMAKR RFF QYFDQL RQLRMWKMQL LDENHLFIKY TSEDVVTLRV TDPSQASFFV VYNMVTTEVI AVFENTSDEL LELFENFCDL FRNA TLHSE VQFPCSASSN NFARQIQRRF KDTIINAKYG GHTEAVRRLL GQLPISAQSY SGSPYLDLSL FSYDDKWVSV MERPK TCGD HPIRFYARDS GLLKFEIQAG LLGRPINHTV RRLVAFTFHP FEPFAISVQR TNAEYVVNFH MRHCCT

UniProtKB: DET1 homolog

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Macromolecule #2: DNA damage-binding protein 1

MacromoleculeName: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 127.097469 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK IAVMELFRPK GESKDLLFIL TAKYNACIL EYKQSGESID IITRAHGNVQ DRIGRPSETG IIGIIDPECR MIGLRLYDGL FKVIPLDRDN KELKAFNIRL E ELHVIDVK ...String:
MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK IAVMELFRPK GESKDLLFIL TAKYNACIL EYKQSGESID IITRAHGNVQ DRIGRPSETG IIGIIDPECR MIGLRLYDGL FKVIPLDRDN KELKAFNIRL E ELHVIDVK FLYGCQAPTI CFVYQDPQGR HVKTYEVSLR EKEFNKGPWK QENVEAEASM VIAVPEPFGG AIIIGQESIT YH NGDKYLA IAPPIIKQST IVCHNRVDPN GSRYLLGDME GRLFMLLLEK EEQMDGTVTL KDLRVELLGE TSIAECLTYL DNG VVFVGS RLGDSQLVKL NVDSNEQGSY VVAMETFTNL GPIVDMCVVD LERQGQGQLV TCSGAFKEGS LRIIRNGIGI HEHA SIDLP GIKGLWPLRS DPNRETDDTL VLSFVGQTRV LMLNGEEVEE TELMGFVDDQ QTFFCGNVAH QQLIQITSAS VRLVS QEPK ALVSEWKEPQ AKNISVASCN SSQVVVAVGR ALYYLQIHPQ ELRQISHTEM EHEVACLDIT PLGDSNGLSP LCAIGL WTD ISARILKLPS FELLHKEMLG GEIIPRSILM TTFESSHYLL CALGDGALFY FGLNIETGLL SDRKKVTLGT QPTVLRT FR SLSTTNVFAC SDRPTVIYSS NHKLVFSNVN LKEVNYMCPL NSDGYPDSLA LANNSTLTIG TIDEIQKLHI RTVPLYES P RKICYQEVSQ CFGVLSSRIE VQDTSGGTTA LRPSASTQAL SSSVSSSKLF SSSTAPHETS FGEEVEVHNL LIIDQHTFE VLHAHQFLQN EYALSLVSCK LGKDPNTYFI VGTAMVYPEE AEPKQGRIVV FQYSDGKLQT VAEKEVKGAV YSMVEFNGKL LASINSTVR LYEWTTEKEL RTECNHYNNI MALYLKTKGD FILVGDLMRS VLLLAYKPME GNFEEIARDF NPNWMSAVEI L DDDNFLGA ENAFNLFVCQ KDSAATTDEE RQHLQEVGLF HLGEFVNVFC HGSLVMQNLG ETSTPTQGSV LFGTVNGMIG LV TSLSESW YNLLLDMQNR LNKVIKSVGK IEHSFWRSFH TERKTEPATG FIDGDLIESF LDISRPKMQE VVANLQYDDG SGM KREATA DDLIKVVEEL TRIH

UniProtKB: DNA damage-binding protein 1

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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: Homo sapiens (human)
SequenceString:
MADFLKGLPV YNKSNFSRFH ADSVCKASNR RPSVYLPTRE YPSEQIIVTE KTNILLRYLH QQWDKKNAAK KRDQEQVELE GESSAPPRK VARTDSPDMH EDT

UniProtKB: DET1- and DDB1-associated protein 1

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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

Concentration0.3 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE
Detailsthe 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

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 46.55 e/Å2
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.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6dsz

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 401370
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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