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- PDB-9bjz: Structure of the human DDD-Ube2e2 complex -

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Basic information

Entry
Database: PDB / ID: 9bjz
TitleStructure of the human DDD-Ube2e2 complex
Components
  • DET1 homolog
  • DET1- and DDB1-associated protein 1
  • DNA damage-binding protein 1
  • Ubiquitin-conjugating enzyme E2 E2
KeywordsPROTEIN BINDING / DDB1 / DDA1 / DET1 / DCAF / ubiquitin conjugating enzyme
Function / homology
Function and homology information


ISG15 transferase activity / ISG15-protein conjugation / regulation of natural killer cell activation / 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 / regulation of natural killer cell activation / 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 / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / negative regulation of reproductive process / negative regulation of developmental process / Cul4B-RING E3 ubiquitin ligase complex / ectopic germ cell programmed cell death / ubiquitin conjugating enzyme activity / ubiquitin ligase complex scaffold activity / viral release from host cell / protein monoubiquitination / cullin family protein binding / positive regulation of G1/S transition of mitotic cell cycle / protein K63-linked ubiquitination / positive regulation of viral genome replication / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / positive regulation of gluconeogenesis / sperm end piece / sperm principal piece / nucleotide-excision repair / proteasomal protein catabolic process / Recognition of DNA damage by PCNA-containing replication complex / regulation of circadian rhythm / Wnt signaling pathway / 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 / cellular response to UV / ubiquitin-protein transferase activity / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / rhythmic process / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / sperm midpiece / Antigen processing: Ubiquitination & Proteasome degradation / site of double-strand break / Neddylation / protein-containing complex assembly / damaged DNA binding / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / chromosome, telomeric region / protein ubiquitination / DNA repair / ubiquitin protein ligase binding / apoptotic process / DNA damage response / nucleolus / negative regulation of apoptotic process / protein-containing complex binding / protein-containing complex / DNA binding / : / 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 / : / 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 / 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 / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsLoughran, T. / Turk, L.S. / Brown, S.H.J. / Mace, P.D.
Funding support New Zealand, 1items
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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA damage-binding protein 1
B: DET1 homolog
C: DET1- and DDB1-associated protein 1
D: Ubiquitin-conjugating enzyme E2 E2


Theoretical massNumber of molelcules
Total (without water)199,4494
Polymers199,4494
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: 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: 95337.336 Da / Num. of mol.: 1 / Mutation: residues 396-705 replaced with GNGNSG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16531
#2: Protein DET1 homolog / De-etiolated-1 homolog


Mass: 67903.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DET1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q7L5Y6
#3: Protein DET1- and DDB1-associated protein 1 / Placenta cross-immune reaction antigen 1 / PCIA-1


Mass: 11855.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDA1, C19orf58, PCIA1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BW61
#4: Protein Ubiquitin-conjugating enzyme E2 E2 / E2 ubiquitin-conjugating enzyme E2 / UbcH8 / Ubiquitin carrier protein E2 / Ubiquitin-protein ligase E2


Mass: 24352.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2E2, UBCH8 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q96LR5, E2 ubiquitin-conjugating enzyme
Has protein modificationY

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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

Component
IDNameTypeEntity IDParent-IDSource
1Complex of DDB1(deltaBPB)-DET1-DDA1-Ube2e2COMPLEXall0MULTIPLE SOURCES
2DDD ComplexCOMPLEX#1-#31RECOMBINANT
3Ube2e2COMPLEX#41RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
32Homo sapiens (human)9606
43Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
32Spodoptera frugiperda (fall armyworm)7108
43Escherichia coli BL21(DE3) (bacteria)469008
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 80 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61234 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 151.64 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002612255
ELECTRON MICROSCOPYf_angle_d0.50916614
ELECTRON MICROSCOPYf_chiral_restr0.04271872
ELECTRON MICROSCOPYf_plane_restr0.00462151
ELECTRON MICROSCOPYf_dihedral_angle_d3.79971655

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