9BJZ | pdb_00009bjz

Structure of the human DDD-Ube2e2 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

DET1 dynamics underlie cooperative ubiquitination by CRL4 DET1-COP1 complexes.

Burgess, A.E.Loughran, T.A.Turk, L.S.Nyvall, H.G.Dunlop, J.L.Jamieson, S.A.Curry, J.R.Burke, J.E.Filipcik, P.Brown, S.H.J.Mace, P.D.

(2025) Sci Adv 11: eadq4187-eadq4187

  • DOI: https://doi.org/10.1126/sciadv.adq4187
  • Primary Citation of Related Structures:  
    9BJZ

  • PubMed 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 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 DET1-COP1 complex assembly, which can affect degradation of diverse targets by COP1 complexes.


  • Organizational Affiliation
    • Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA damage-binding protein 1853Homo sapiensMutation(s): 0 
Gene Names: DDB1XAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens)
Explore Q16531 
Go to UniProtKB:  Q16531
PHAROS:  Q16531
GTEx:  ENSG00000167986 
Entity Groups  
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UniProt GroupQ16531
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DET1 homolog589Homo sapiensMutation(s): 0 
Gene Names: DET1
UniProt & NIH Common Fund Data Resources
Find proteins for Q7L5Y6 (Homo sapiens)
Explore Q7L5Y6 
Go to UniProtKB:  Q7L5Y6
PHAROS:  Q7L5Y6
GTEx:  ENSG00000140543 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7L5Y6
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DET1- and DDB1-associated protein 1102Homo sapiensMutation(s): 0 
Gene Names: DDA1C19orf58PCIA1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BW61 (Homo sapiens)
Explore Q9BW61 
Go to UniProtKB:  Q9BW61
PHAROS:  Q9BW61
GTEx:  ENSG00000130311 
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UniProt GroupQ9BW61
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 E2220Homo sapiensMutation(s): 0 
Gene Names: UBE2E2UBCH8
EC: 2.3.2.23
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Find proteins for Q96LR5 (Homo sapiens)
Explore Q96LR5 
Go to UniProtKB:  Q96LR5
PHAROS:  Q96LR5
GTEx:  ENSG00000182247 
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UniProt GroupQ96LR5
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Marsden FundNew ZealandUOO2102

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release
  • Version 1.1: 2025-03-12
    Changes: Data collection, Database references