8IRQ | pdb_00008irq

Larimichthys crocea IFNd

  • Classification: CYTOKINE
  • Organism(s): Larimichthys crocea
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2023-03-19 Released: 2024-03-20 
  • Deposition Author(s): Chen, J.J.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 
    0.219 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.162 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.164 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and Functional Characterization of a Fish Type I Subgroup d IFN Reveals Its Binding to Receptors.

Guan, Y.Chen, J.Guan, H.Chen, T.T.Teng, Y.Wei, Z.Li, Z.Ouyang, S.Chen, X.

(2024) J Immunol 212: 1207-1220

  • DOI: https://doi.org/10.4049/jimmunol.2300651
  • Primary Citation of Related Structures:  
    7WZ5, 8IRQ

  • PubMed Abstract: 

    Teleost fish type I IFNs and the associated receptors from the cytokine receptor family B (CRFB) are characterized by remarkable diversity and complexity. How the fish type I IFNs bind to their receptors is still not fully understood. In this study, we demonstrate that CRFB1 and CRFB5 constitute the receptor pair through which type I subgroup d IFN (IFNd) from large yellow croaker, Larimichthys crocea, activates the conserved JAK-STAT signaling pathway as a part of the antiviral response. Our data suggest that L. crocea IFNd (LcIFNd) has a higher binding affinity with L. crocea CRFB5 (LcCRFB5) than with LcCRFB1. Furthermore, we report the crystal structure of LcIFNd at a 1.49-Å resolution and construct structural models of LcIFNd in binary complexes with predicted structures of extracellular regions of LcCRFB1 and LcCRFB5, respectively. Despite striking similarities in overall architectures of LcIFNd and its ortholog human IFN-ω, the receptor binding patterns between LcIFNd and its receptors show that teleost and mammalian type I IFNs may have differentially selected helices that bind to their homologous receptors. Correspondingly, key residues mediating binding of LcIFNd to LcCRFB1 and LcCRFB5 are largely distinct from the receptor-interacting residues in other fish and mammalian type I IFNs. Our findings reveal a ligand/receptor complex binding mechanism of IFNd in teleost fish, thus providing new insights into the function and evolution of type I IFNs.


  • Organizational Affiliation
    • State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Interferon d165Larimichthys croceaMutation(s): 0 
UniProt
Find proteins for A0A1L4AIP8 (Larimichthys crocea)
Explore A0A1L4AIP8 
Go to UniProtKB:  A0A1L4AIP8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1L4AIP8
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free:  0.219 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.162 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.164 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.378α = 90
b = 38.813β = 112.82
c = 51.091γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
HKL-2000data scaling
SHELXTphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2024-03-20 
  • Deposition Author(s): Chen, J.J.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-20
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Structure summary
  • Version 1.2: 2025-10-01
    Changes: Database references