6NII

Crystal structure of RavD (residues 1-200) from Legionella pneumophila (strain Corby)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report

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This is version 1.4 of the entry. See complete history


Literature

A bacterial effector deubiquitinase specifically hydrolyses linear ubiquitin chains to inhibit host inflammatory signalling.

Wan, M.Wang, X.Huang, C.Xu, D.Wang, Z.Zhou, Y.Zhu, Y.

(2019) Nat Microbiol 4: 1282-1293

  • DOI: https://doi.org/10.1038/s41564-019-0454-1
  • Primary Citation of Related Structures:  
    6NII, 6NJD

  • PubMed Abstract: 

    Linear ubiquitin (Ub) chains regulate many cellular processes, including NF-κB immune signalling. Pathogenic bacteria have evolved to secrete effector proteins that harbour deubiquitinase activity into host cells to disrupt host ubiquitination signalling. All previously identified effector deubiquitinases hydrolyse isopeptide-linked polyubiquitin (polyUb). It has been a long-standing question whether bacterial pathogens have evolved an effector deubiquitinase to directly cleave linear Ub chains. In this study, we performed extensive screening of bacterial pathogens and found that Legionella pneumophila-the causative agent of human Legionnaire's disease-encodes an effector protein, RavD, which harbours deubiquitinase activity exquisitely specific for linear Ub chains. RavD hydrolyses linear Ub chains but not any type of isopeptide-linked polyUb. The crystal structure of RavD with linear diubiquitin reveals that RavD adopts a papain-like fold with a Cys-His-Ser catalytic triad. The Ub-binding surface and specific interacting residues in RavD determine its specificity for Met1 linkages. RavD prevents the accumulation of linear Ub chains on Legionella-containing vacuoles established by the pathogen in host cells to inhibit the NF-κB pathway during infection. This study identified a unique linear Ub chain-specific effector deubiquitinase and indicates its potential application as a tool to dissect linear polyUb-mediated signalling in mammalian cells.


  • Organizational Affiliation

    MOE Key Laboratory of Biosystems Homeostasis & Protection, Innovation Center for Cell Signalling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein RavDA [auth B],
B [auth A]
205Legionella pneumophilaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.335α = 90
b = 142.335β = 90
c = 55.215γ = 120
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81530068
National Natural Science Foundation of China (NSFC)China81322024
National Natural Science Foundation of China (NSFC)China31370722
National Natural Science Foundation of China (NSFC)China81561130162
National Natural Science Foundation of China (NSFC)China81501717
Ministry of Science and Technology (MoST, China)China2017YFA0503900
Royal SocietyUnited KingdomNA140239

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-06-05
    Changes: Data collection, Database references
  • Version 1.2: 2019-08-07
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description