3WXG

Crystal structure of CYLD USP domain (C596A) in complex with Lys63-linked diubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structures of CYLD USP with Met1- or Lys63-linked diubiquitin reveal mechanisms for dual specificity.

Sato, Y.Goto, E.Shibata, Y.Kubota, Y.Yamagata, A.Goto-Ito, S.Kubota, K.Inoue, J.Takekawa, M.Tokunaga, F.Fukai, S.

(2015) Nat Struct Mol Biol 22: 222-229

  • DOI: https://doi.org/10.1038/nsmb.2970
  • Primary Citation of Related Structures:  
    3WXE, 3WXF, 3WXG

  • PubMed Abstract: 

    The tumor suppressor CYLD belongs to a ubiquitin (Ub)-specific protease (USP) family and specifically cleaves Met1- and Lys63-linked polyubiquitin chains to suppress inflammatory signaling pathways. Here, we report crystal structures representing the catalytic states of zebrafish CYLD for Met1- and Lys63-linked Ub chains and two distinct precatalytic states for Met1-linked chains. In both catalytic states, the distal Ub is bound to CYLD in a similar manner, and the scissile bond is located close to the catalytic residue, whereas the proximal Ub is bound in a manner specific to Met1- or Lys63-linked chains. Further structure-based mutagenesis experiments support the mechanism by which CYLD specifically cleaves both Met1- and Lys63-linked chains and provide insight into tumor-associated mutations of CYLD. This study provides new structural insight into the mechanisms by which USP family deubiquitinating enzymes recognize and cleave Ub chains with specific linkage types.


  • Organizational Affiliation

    1] Life Science Division, Synchrotron Radiation Research Organization, University of Tokyo, Tokyo, Japan. [2] Center for Structural Biology of Challenging Proteins, Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo, Japan. [3] Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein
A, D
312Danio rerioMutation(s): 1 
Gene Names: CYLDcylda
EC: 3.4.19.12
UniProt
Find proteins for E7FEV5 (Danio rerio)
Explore E7FEV5 
Go to UniProtKB:  E7FEV5
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UniProt GroupE7FEV5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin
B, E
76Mus musculusMutation(s): 1 
Gene Names: Ubc
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG50 (Mus musculus)
Explore P0CG50 
Go to UniProtKB:  P0CG50
IMPC:  MGI:98889
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CG50
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin
C, F
72Mus musculusMutation(s): 0 
Gene Names: Ubc
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG50 (Mus musculus)
Explore P0CG50 
Go to UniProtKB:  P0CG50
IMPC:  MGI:98889
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CG50
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.017α = 103.49
b = 65.657β = 89.86
c = 69.821γ = 90.61
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-11
    Type: Initial release
  • Version 1.1: 2017-08-16
    Changes: Refinement description, Source and taxonomy
  • Version 1.2: 2020-01-01
    Changes: Database references
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Refinement description