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 

Starting Models: experimental
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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)
Explore P63208 
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 
Entity Groups  
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UniProt GroupQ9UF56
Sequence Annotations
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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
Sequence Annotations
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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