6WCQ

Structure of a substrate-bound DQC ubiquitin ligase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for dimerization quality control.

Mena, E.L.Jevtic, P.Greber, B.J.Gee, C.L.Lew, B.G.Akopian, D.Nogales, E.Kuriyan, J.Rape, M.

(2020) Nature 586: 452-456

  • DOI: https://doi.org/10.1038/s41586-020-2636-7
  • Primary Citation of Related Structures:  
    6W66, 6W67, 6W68, 6W69, 6WCQ

  • PubMed Abstract: 

    Most quality control pathways target misfolded proteins to prevent toxic aggregation and neurodegeneration 1 . Dimerization quality control further improves proteostasis by eliminating complexes of aberrant composition 2 , but how it detects incorrect subunits remains unknown. Here we provide structural insight into target selection by SCF-FBXL17, a dimerization-quality-control E3 ligase that ubiquitylates and helps to degrade inactive heterodimers of BTB proteins while sparing functional homodimers. We find that SCF-FBXL17 disrupts aberrant BTB dimers that fail to stabilize an intermolecular β-sheet around a highly divergent β-strand of the BTB domain. Complex dissociation allows SCF-FBXL17 to wrap around a single BTB domain, resulting in robust ubiquitylation. SCF-FBXL17 therefore probes both shape and complementarity of BTB domains, a mechanism that is well suited to establish quality control of complex composition for recurrent interaction modules.


  • Organizational Affiliation

    Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S-phase kinase-associated protein 1163Homo sapiensMutation(s): 0 
Gene Names: SKP1EMC19OCP2SKP1ATCEB1L
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Find proteins for P63208 (Homo sapiens)
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Go to UniProtKB:  P63208
PHAROS:  P63208
GTEx:  ENSG00000113558 
Entity Groups  
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UniProt GroupP63208
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
F-box/LRR-repeat protein 17396Homo sapiensMutation(s): 0 
Gene Names: FBXL17FBL17FBX13FBXO13
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UF56 (Homo sapiens)
Explore Q9UF56 
Go to UniProtKB:  Q9UF56
PHAROS:  Q9UF56
GTEx:  ENSG00000145743 
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UniProt GroupQ9UF56
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Kelch-like ECH-associated protein 1631Homo sapiensMutation(s): 1 
Gene Names: KEAP1INRF2KIAA0132KLHL19
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Find proteins for Q14145 (Homo sapiens)
Explore Q14145 
Go to UniProtKB:  Q14145
PHAROS:  Q14145
GTEx:  ENSG00000079999 
Entity Groups  
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UniProt GroupQ14145
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cullin-1434Homo sapiensMutation(s): 0 
Gene Names: CUL1
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Find proteins for Q13616 (Homo sapiens)
Explore Q13616 
Go to UniProtKB:  Q13616
PHAROS:  Q13616
GTEx:  ENSG00000055130 
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UniProt GroupQ13616
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-19
    Type: Initial release
  • Version 1.1: 2020-09-02
    Changes: Database references
  • Version 1.2: 2020-10-28
    Changes: Database references
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references, Refinement description