6LHF | pdb_00006lhf

Crystal structure of chicken cCD8aa/pBF2*15:01


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.299 (Depositor), 0.306 (DCC) 
  • R-Value Work: 
    0.253 (Depositor), 0.265 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

The Combination of CD8 alpha alpha and Peptide-MHC-I in a Face-to-Face Mode Promotes Chicken gamma delta T Cells Response.

Liu, Y.Chen, R.Liang, R.Sun, B.Wu, Y.Zhang, L.Kaufman, J.Xia, C.

(2020) Front Immunol 11: 605085-605085

  • DOI: https://doi.org/10.3389/fimmu.2020.605085
  • Primary Citation Related Structures: 
    6LHF, 6LHG, 6LHH

  • PubMed Abstract: 

    The CD8αα homodimer is crucial to both thymic T cell selection and the antigen recognition of cytotoxic T cells. The CD8-pMHC-I interaction can enhance CTL immunity via stabilizing the TCR-pMHC-I interaction and optimizing the cross-reactivity and Ag sensitivity of CD8 + T cells at various stages of development. To date, only human and mouse CD8-pMHC-I complexes have been determined. Here, we resolved the pBF2*1501 complex and the cCD8αα/pBF2*1501 and cCD8αα/pBF2*0401 complexes in nonmammals for the first time. Remarkably, cCD8αα/pBF2*1501 and the cCD8αα/pBF2*0401 complex both exhibited two binding modes, including an "antibody-like" mode similar to that of the known mammal CD8/pMHC-I complexes and a "face-to-face" mode that has been observed only in chickens to date. Compared to the "antibody-like" mode, the "face-to-face" binding mode changes the binding orientation of the cCD8αα homodimer to pMHC-I, which might facilitate abundant γδT cells to bind diverse peptides presented by limited BF2 alleles in chicken. Moreover, the forces involving in the interaction of cCD8αα/pBF2*1501 and the cCD8αα/pBF2*0401 are different in this two binding model, which might change the strength of the CD8-pMHC-I interaction, amplifying T cell cross-reactivity in chickens. The coreceptor CD8αα of TCR has evolved two peptide-MHC-I binding patterns in chickens, which might enhance the T cell response to major or emerging pathogens, including chicken-derived pathogens that are relevant to human health, such as high-pathogenicity influenza viruses.


  • Organizational Affiliation
    • Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 137.19 kDa 
  • Atom Count: 9,764 
  • Modeled Residue Count: 1,196 
  • Deposited Residue Count: 1,196 
  • Unique protein chains: 4

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MHC class IA,
F [auth D]
270Gallus gallusMutation(s): 0 
Gene Names: BF2
UniProt
Find proteins for Q9GIP6 (Gallus gallus)
Explore Q9GIP6 
Go to UniProtKB:  Q9GIP6
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UniProt GroupQ9GIP6
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulinB,
G [auth E]
96Gallus gallusMutation(s): 0 
Gene Names: B2M
UniProt
Find proteins for P21611 (Gallus gallus)
Explore P21611 
Go to UniProtKB:  P21611
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UniProt GroupP21611
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
RY0808 peptideC,
H [auth F]
8Gallus gallusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
CD8 alpha chainD [auth G],
E [auth H],
I,
J
112Gallus gallusMutation(s): 0 
Gene Names: CD8
UniProt
Find proteins for Q6QR64 (Gallus gallus)
Explore Q6QR64 
Go to UniProtKB:  Q6QR64
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UniProt GroupQ6QR64
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.299 (Depositor), 0.306 (DCC) 
  • R-Value Work:  0.253 (Depositor), 0.265 (DCC) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.34α = 84.595
b = 66.735β = 82.041
c = 103.949γ = 67.506
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31572493
National Natural Science Foundation of China (NSFC)China31972683

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-09
    Type: Initial release
  • Version 1.1: 2021-06-23
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary