7OKQ

Cryo-EM Structure of the DDB1-DCAF1-CUL4A-RBX1 Complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The CRL4 DCAF1 cullin-RING ubiquitin ligase is activated following a switch in oligomerization state.

Mohamed, W.I.Schenk, A.D.Kempf, G.Cavadini, S.Basters, A.Potenza, A.Abdul Rahman, W.Rabl, J.Reichermeier, K.Thoma, N.H.

(2021) EMBO J 40: e108008-e108008

  • DOI: 10.15252/embj.2021108008
  • Primary Citation of Related Structures:  
    7OKQ

  • PubMed Abstract: 
  • The cullin-4-based RING-type (CRL4) family of E3 ubiquitin ligases functions together with dedicated substrate receptors. Out of the ˜29 CRL4 substrate receptors reported, the DDB1- and CUL4-associated factor 1 (DCAF1) is essential for cellular survival and growth, and its deregulation has been implicated in tumorigenesis ...

    The cullin-4-based RING-type (CRL4) family of E3 ubiquitin ligases functions together with dedicated substrate receptors. Out of the ˜29 CRL4 substrate receptors reported, the DDB1- and CUL4-associated factor 1 (DCAF1) is essential for cellular survival and growth, and its deregulation has been implicated in tumorigenesis. We carried out biochemical and structural studies to examine the structure and mechanism of the CRL4 DCAF1 ligase. In the 8.4 Å cryo-EM map of CRL4 DCAF1 , four CUL4-RBX1-DDB1-DCAF1 protomers are organized into two dimeric sub-assemblies. In this arrangement, the WD40 domain of DCAF1 mediates binding with the cullin C-terminal domain (CTD) and the RBX1 subunit of a neighboring CRL4 DCAF1 protomer. This renders RBX1, the catalytic subunit of the ligase, inaccessible to the E2 ubiquitin-conjugating enzymes. Upon CRL4 DCAF1 activation by neddylation, the interaction between the cullin CTD and the neighboring DCAF1 protomer is broken, and the complex assumes an active dimeric conformation. Accordingly, a tetramerization-deficient CRL4 DCAF1 mutant has higher ubiquitin ligase activity compared to the wild-type. This study identifies a novel mechanism by which unneddylated and substrate-free CUL4 ligases can be maintained in an inactive state.


    Organizational Affiliation

    Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA damage-binding protein 1A, E, I, M1,159Homo sapiensMutation(s): 0 
Gene Names: DDB1XAP1
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Find proteins for Q16531 (Homo sapiens)
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PHAROS:  Q16531
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UniProt GroupQ16531
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DDB1- and CUL4-associated factor 1B, F, J, N1,525Homo sapiensMutation(s): 0 
Gene Names: DCAF1KIAA0800RIPVPRBP
EC: 2.7.11.1
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UniProt GroupQ9Y4B6
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cullin-4AC, G, K, O742Homo sapiensMutation(s): 0 
Gene Names: CUL4A
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Find proteins for Q13619 (Homo sapiens)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RBX1D, H, L, P116Homo sapiensMutation(s): 0 
Gene Names: RBX1RNF75ROC1
EC: 2.3.2.27 (PDB Primary Data), 2.3.2.32 (PDB Primary Data)
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UniProt GroupP62877
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-13
    Type: Initial release
  • Version 1.1: 2021-11-24
    Changes: Database references
  • Version 1.2: 2021-12-01
    Changes: Database references