6LAN

Structure of CCDC50 and LC3B complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A novel selective autophagy receptor, CCDC50, delivers K63 polyubiquitination-activated RIG-I/MDA5 for degradation during viral infection.

Hou, P.Yang, K.Jia, P.Liu, L.Lin, Y.Li, Z.Li, J.Chen, S.Guo, S.Pan, J.Wu, J.Peng, H.Zeng, W.Li, C.Liu, Y.Guo, D.

(2021) Cell Res 31: 62-79

  • DOI: https://doi.org/10.1038/s41422-020-0362-1
  • Primary Citation of Related Structures:  
    6LAN

  • PubMed Abstract: 

    Autophagy is a conserved process that delivers cytosolic substances to the lysosome for degradation, but its direct role in the regulation of antiviral innate immunity remains poorly understood. Here, through high-throughput screening, we discovered that CCDC50 functions as a previously unknown autophagy receptor that negatively regulates the type I interferon (IFN) signaling pathway initiated by RIG-I-like receptors (RLRs), the sensors for RNA viruses. The expression of CCDC50 is enhanced by viral infection, and CCDC50 specifically recognizes K63-polyubiquitinated RLRs, thus delivering the activated RIG-I/MDA5 for autophagic degradation. The association of CCDC50 with phagophore membrane protein LC3 is confirmed by crystal structure analysis. In contrast to other known autophagic cargo receptors that associate with either the LIR-docking site (LDS) or the UIM-docking site (UDS) of LC3, CCDC50 can bind to both LDS and UDS, representing a new type of cargo receptor. In mouse models with RNA virus infection, CCDC50 deficiency reduces the autophagic degradation of RIG-I/MDA5 and promotes type I IFN responses, resulting in enhanced viral resistance and improved survival rates. These results reveal a new link between autophagy and antiviral innate immune responses and provide additional insights into the regulatory mechanisms of RLR-mediated antiviral signaling.


  • Organizational Affiliation

    MOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Studies (CIIS), Seventh Affiliated Hospital, School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, 518107, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Coiled-coil domain-containing protein 50,Microtubule-associated proteins 1A/1B light chain 3B135Homo sapiensMutation(s): 0 
Gene Names: CCDC50C3orf6MAP1LC3BMAP1ALC3
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IVM0 (Homo sapiens)
Explore Q8IVM0 
Go to UniProtKB:  Q8IVM0
PHAROS:  Q8IVM0
GTEx:  ENSG00000152492 
Find proteins for Q9GZQ8 (Homo sapiens)
Explore Q9GZQ8 
Go to UniProtKB:  Q9GZQ8
PHAROS:  Q9GZQ8
GTEx:  ENSG00000140941 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ9GZQ8Q8IVM0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.776α = 90
b = 46.804β = 101.269
c = 46.154γ = 90
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2021-01-20
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description