9HYG | pdb_00009hyg

Crystal structure of zebrafish S100I1 in Na+-bound form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.232 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Teleost-specific ictacalcins exhibit similar structural organization, cation-dependent activation, and transcriptional regulation as human S100 proteins.

Hernandez, L.Paris, T.Demou, M.Birck, C.Begon-Pescia, C.Rodriguez Vidal, J.F.Tyrkalska, S.D.Bureau, C.Gonzalez, C.Gracia, J.Lelievre, E.Mulero, V.Nguyen-Chi, M.Yatime, L.

(2025) FEBS J 

  • DOI: https://doi.org/10.1111/febs.70354
  • Primary Citation of Related Structures:  
    9HYG, 9I1G, 9I2N

  • PubMed Abstract: 

    S100 proteins are highly versatile calcium-binding proteins from vertebrates. Following extracellular release, they become essential in immune and antimicrobial defenses, initiating the inflammatory response through receptor signaling and providing direct control of bacterial invaders via nutritional immunity. While mammalian S100s have been extensively studied, very little is known about the more recently discovered S100 proteins from teleost fish, including those with no strict orthologs in mammals. Comparable functioning between both clades would allow us to expand their study into the highly popular zebrafish model, which is particularly suited for live imaging and mechanistic exploration of immune and inflammatory processes. To fill the gap of knowledge on teleost S100s, we here provide detailed structural and biochemical characterization of S100i1 and S100i2 from Danio rerio, two teleost-specific S100s absent in mammals. We demonstrate that they nevertheless share conserved tertiary and quaternary organization with mammalian S100s. In addition, they exhibit comparable calcium binding properties and undergo a similar calcium-dependent activation mechanism. Furthermore, they display analogous expression patterns, being enriched in tissues highly exposed to the environment such as gills and skin, the latter constituting an important reservoir of S100 proteins in mammals. Finally, our results show, for the very first time, that s100i2/i2 gene expression is differentially modulated in sterile disease conditions associated with sustained inflammation or a high hypoxic state. Altogether, these findings underline the strong parallelism existing between mammalian and teleost-specific S100 proteins despite their divergent evolution, opening up new avenues to explore their biology in the zebrafish model.


  • Organizational Affiliation
    • Laboratory of Pathogens and Host Immunity (LPHI), University of Montpellier, INSERM UA15, CNRS UMR5294, France.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein S100
A, B
97Danio rerioMutation(s): 0 
Gene Names: icnfa91d07mg:cb02f02s100a4awu:fa91d07
UniProt
Find proteins for Q6XG62 (Danio rerio)
Explore Q6XG62 
Go to UniProtKB:  Q6XG62
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6XG62
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.232 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.23α = 90
b = 55.86β = 100
c = 45.02γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
BALBESphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
H2020 Marie Curie Actions of the European CommissionEuropean Union955576

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-03
    Type: Initial release
  • Version 1.1: 2025-12-10
    Changes: Database references