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- EMDB-63375: Cryo-EM structure of dimeric DDB1-DDA1-DET1-Ube2e2-COP1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-63375
TitleCryo-EM structure of dimeric DDB1-DDA1-DET1-Ube2e2-COP1 complex
Map datafull map
Sample
  • Complex: protein complex of dimeric DDB1-DDA1-DET1-Ube2e2-COP1
    • Protein or peptide: E3 ubiquitin-protein ligase COP1
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: DET1 homolog
    • Protein or peptide: DET1- and DDB1-associated protein 1
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 E2
KeywordsE3 ligase component / LIGASE
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 / protein K11-linked ubiquitination / 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 ...ISG15 transferase activity / ISG15-protein conjugation / cullin-RING ubiquitin ligase complex / positive regulation by virus of viral protein levels in host cell / protein K11-linked ubiquitination / 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 / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / response to ionizing radiation / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / ubiquitin conjugating enzyme activity / negative regulation of reproductive process / negative regulation of developmental process / viral release from host cell / cullin family protein binding / protein K63-linked ubiquitination / protein monoubiquitination / positive regulation of G1/S transition of mitotic cell cycle / ectopic germ cell programmed cell death / positive regulation of viral genome replication / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / proteasomal protein catabolic process / positive regulation of gluconeogenesis / nucleotide-excision repair / Autodegradation of the E3 ubiquitin ligase COP1 / Recognition of DNA damage by PCNA-containing replication complex / regulation of circadian rhythm / RING-type E3 ubiquitin transferase / 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 / ubiquitin-protein transferase activity / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of protein catabolic process / ubiquitin protein ligase activity / 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 / nuclear speck / protein ubiquitination / Golgi membrane / 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 / zinc ion binding / nucleoplasm / 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) / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal ...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) / 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 / 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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 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_63375.png

Downloads & links

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Map

FileDownload / File: emd_63375.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull map
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 560 pix.
= 476. Å		0.85 Å/pix.
x 560 pix.
= 476. Å		0.85 Å/pix.
x 560 pix.
= 476. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.0615
Minimum - Maximum-0.34595135 - 0.9121287
Average (Standard dev.)-0.0002712716 (±0.021134976)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 476.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: deepemhancer post-processing map

Fileemd_63375_additional_1.map
Annotationdeepemhancer post-processing map
Projections & Slices
AxesZYX

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Half map: half map - A

Fileemd_63375_half_map_1.map
Annotationhalf map - A
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Histogram

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Half map: half map - B

Fileemd_63375_half_map_2.map
Annotationhalf map - B
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Sample components

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Entire : protein complex of dimeric DDB1-DDA1-DET1-Ube2e2-COP1

EntireName: protein complex of dimeric DDB1-DDA1-DET1-Ube2e2-COP1
Components
  • Complex: protein complex of dimeric DDB1-DDA1-DET1-Ube2e2-COP1
    • Protein or peptide: E3 ubiquitin-protein ligase COP1
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: DET1 homolog
    • Protein or peptide: DET1- and DDB1-associated protein 1
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 E2

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Supramolecule #1: protein complex of dimeric DDB1-DDA1-DET1-Ube2e2-COP1

SupramoleculeName: protein complex of dimeric DDB1-DDA1-DET1-Ube2e2-COP1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 600 KDa

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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: 2 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 80.569242 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSGSRQAGSG SAGTSPGSSA ASSVTSASSS LSSSPSPPSV AVSAAALVSG GVAQAAGSGG LGGPVRPVLV APAVSGSGGG AVSTGLSRH SCAARPSAGV GGSSSSLGSG SRKRPLLAPL CNGLINSYED KSNDFVCPIC FDMIEEAYMT KCGHSFCYKC I HQSLEDNN ...String:
MSGSRQAGSG SAGTSPGSSA ASSVTSASSS LSSSPSPPSV AVSAAALVSG GVAQAAGSGG LGGPVRPVLV APAVSGSGGG AVSTGLSRH SCAARPSAGV GGSSSSLGSG SRKRPLLAPL CNGLINSYED KSNDFVCPIC FDMIEEAYMT KCGHSFCYKC I HQSLEDNN RCPKCNYVVD NIDHLYPNFL VNELILKQKQ RFEEKRFKLD HSVSSTNGHR WQIFQDWLGT DQDNLDLANV NL MLELLVQ KKKQLEAESH AAQLQILMEF LKVARRNKRE QLEQIQKELS VLEEDIKRVE EMSGLYSPVS EDSTVPQFEA PSP SHSSII DSTEYSQPPG FSGSSQTKKQ PWYNSTLASR RKRLTAHFED LEQCYFSTRM SRISDDSRTA SQLDEFQECL SKFT RYNSV RPLATLSYAS DLYNGSSIVS SIEFDRDCDY FAIAGVTKKI KVYEYDTVIQ DAVDIHYPEN EMTCNSKISC ISWSS YHKN LLASSDYEGT VILWDGFTGQ RSKVYQEHEK RCWSVDFNLM DPKLLASGSD DAKVKLWSTN LDNSVASIEA KANVCC VKF SPSSRYHLAF GCADHCVHYY DLRNTKQPIM VFKGHRKAVS YAKFVSGEEI VSASTDSQLK LWNVGKPYCL RSFKGHI NE KNFVGLASNG DYIACGSENN SLYLYYKGLS KTLLTFKFDT VKSVLDKDRK EDDTNEFVSA VCWRALPDGE SNVLIAAN S QGTIKVLELV

UniProtKB: E3 ubiquitin-protein ligase COP1

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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: 2 / 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 homolog

MacromoleculeName: DET1 homolog / type: protein_or_peptide / ID: 3 / Number of copies: 2 / 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 #4: DET1- and DDB1-associated protein 1

MacromoleculeName: DET1- and DDB1-associated protein 1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / 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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Macromolecule #5: Ubiquitin-conjugating enzyme E2 E2

MacromoleculeName: Ubiquitin-conjugating enzyme E2 E2 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO / EC number: E2 ubiquitin-conjugating enzyme
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.282092 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSTEAQRVDD SPSTSGGSSD GDQRESVQQE PEREQVQPKK KEGKISSKTA AKLSTSAKRI QKELAEITLD PPPNCSAGPK GDNIYEWRS TILGPPGSVY EGGVFFLDIT FSPDYPFKPP KVTFRTRIYH CNINSQGVIC LDILKDNWSP ALTISKVLLS I CSLLTDCN ...String:
MSTEAQRVDD SPSTSGGSSD GDQRESVQQE PEREQVQPKK KEGKISSKTA AKLSTSAKRI QKELAEITLD PPPNCSAGPK GDNIYEWRS TILGPPGSVY EGGVFFLDIT FSPDYPFKPP KVTFRTRIYH CNINSQGVIC LDILKDNWSP ALTISKVLLS I CSLLTDCN PADPLVGSIA TQYMTNRAEH DRMARQWTKR YAT

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

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: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 61817
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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