8HXS | pdb_00008hxs

Small_spotted catshark CD8alpha


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 
    0.216 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.211 (DCC) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

The first crystal structure of CD8 alpha alpha from a cartilaginous fish.

Jia, Z.Feng, J.Dooley, H.Zou, J.Wang, J.

(2023) Front Immunol 14: 1156219-1156219

  • DOI: https://doi.org/10.3389/fimmu.2023.1156219
  • Primary Citation Related Structures: 
    8HXS

  • PubMed Abstract: 

    Cartilaginous fishes are the most evolutionary-distant vertebrates from mammals and possess an immunoglobulin (Ig)- and T cell-mediated adaptive immunity. CD8 is the hallmark receptor of cytotoxic T cells and is required for the formation of T cell receptor-major histocompatibility complex (TCR-MHC) class I complexes. RACE PCR was used to obtain gene sequences. Direct dilution was applied for the refolding of denatured recombinant CD8 protein. Hanging-drop vapor diffusion method was performed for protein crystallization. In this study, CD8α and CD8β orthologues (termed ScCD8α and ScCD8β) were identified in small-spotted catshark ( Scyliorhinus canicula ). Both ScCD8α and ScCD8β possess an extracellular immunoglobulin superfamily (IgSF) V domain as in previously identified CD8 proteins. The genes encoding CD8α and CD8β are tandemly linked in the genomes of all jawed vertebrates studied, suggesting that they were duplicated from a common ancestral gene before the divergence of cartilaginous fishes and other vertebrates. We determined the crystal structure of the ScCD8α ectodomain homodimer at a resolution of 1.35 Å and show that it exhibits the typical topological structure of CD8α from endotherms. As in mammals, the homodimer formation of ScCD8αα relies upon interactions within a hydrophobic core although this differs in position and amino acid composition. Importantly, ScCD8αα shares the canonical cavity required for interaction with peptide-loaded MHC I in mammals. Furthermore, it was found that ScCD8α can co-immunoprecipitate with ScCD8β, indicating that it can form both homodimeric and heterodimeric complexes. Our results expand the current knowledge of vertebrate CD8 dimerization and the interaction between CD8α with p/MHC I from an evolutionary perspective.


  • Organizational Affiliation
    • Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China.

Macromolecule Content 

  • Total Structure Weight: 11.32 kDa 
  • Atom Count: 919 
  • Modeled Residue Count: 100 
  • Deposited Residue Count: 100 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD8 alpha chain100Scyliorhinus caniculaMutation(s): 0 
UniProt
Find proteins for A0A8A5LLJ8 (Scyliorhinus canicula)
Explore A0A8A5LLJ8 
Go to UniProtKB:  A0A8A5LLJ8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8A5LLJ8
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free:  0.216 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.211 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.384α = 90
b = 40.446β = 92.556
c = 32.828γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32030112

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-22
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Data collection, Database references
  • Version 1.2: 2024-04-17
    Changes: Derived calculations
  • Version 1.3: 2024-11-13
    Changes: Structure summary