7OWD

Structure of CYLD CAP-Gly3 (467-552) bound to Ub; tetragonal space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


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Literature

Regulation of CYLD activity and specificity by phosphorylation and ubiquitin-binding CAP-Gly domains.

Elliott, P.R.Leske, D.Wagstaff, J.Schlicher, L.Berridge, G.Maslen, S.Timmermann, F.Ma, B.Fischer, R.Freund, S.M.V.Komander, D.Gyrd-Hansen, M.

(2021) Cell Rep 37: 109777-109777

  • DOI: 10.1016/j.celrep.2021.109777
  • Primary Citation of Related Structures:  
    7OWC, 7OWD

  • PubMed Abstract: 
  • Non-degradative ubiquitin chains and phosphorylation events govern signaling responses by innate immune receptors. The deubiquitinase CYLD in complex with SPATA2 is recruited to receptor signaling complexes by the ubiquitin ligase LUBAC and regulates Met1- and Lys63-linked polyubiquitin and receptor signaling outcomes ...

    Non-degradative ubiquitin chains and phosphorylation events govern signaling responses by innate immune receptors. The deubiquitinase CYLD in complex with SPATA2 is recruited to receptor signaling complexes by the ubiquitin ligase LUBAC and regulates Met1- and Lys63-linked polyubiquitin and receptor signaling outcomes. Here, we investigate the molecular determinants of CYLD activity. We reveal that two CAP-Gly domains in CYLD are ubiquitin-binding domains and demonstrate a requirement of CAP-Gly3 for CYLD activity and regulation of immune receptor signaling. Moreover, we identify a phosphorylation switch outside of the catalytic USP domain, which activates CYLD toward Lys63-linked polyubiquitin. The phosphorylated residue Ser568 is a novel tumor necrosis factor (TNF)-regulated phosphorylation site in CYLD and works in concert with Ser418 to enable CYLD-mediated deubiquitination and immune receptor signaling. We propose that phosphorylated CYLD, together with SPATA2 and LUBAC, functions as a ubiquitin-editing complex that balances Lys63- and Met1-linked polyubiquitin at receptor signaling complexes to promote LUBAC signaling.


    Organizational Affiliation

    Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Off-Roosevelt Drive, Oxford OX3 7DQ, UK; LEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, Maersk Tower, Blegdamsvej 3B, 2200 Copenhagen, Denmark. Electronic address: mgyrd@sund.ku.dk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase CYLDA [auth B]86Homo sapiensMutation(s): 0 
Gene Names: CYLDCYLD1KIAA0849HSPC057
EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NQC7 (Homo sapiens)
Explore Q9NQC7 
Go to UniProtKB:  Q9NQC7
PHAROS:  Q9NQC7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NQC7
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinB [auth A]76Homo sapiensMutation(s): 0 
Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
PHAROS:  P0CG48
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CG48
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.215 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.931α = 90
b = 42.931β = 90
c = 171.338γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomU105192732
Medical Research Council (MRC, United Kingdom)United KingdomMR/R008582/1

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-20
    Type: Initial release