6LIR

crystal structure of chicken TCR for 2.0


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and Biophysical Insights into the TCR alpha beta Complex in Chickens.

Zhang, L.Liu, Y.Meng, G.Liang, R.Zhang, B.Xia, C.

(2020) iScience 23: 101828-101828

  • DOI: https://doi.org/10.1016/j.isci.2020.101828
  • Primary Citation of Related Structures:  
    6LIR

  • PubMed Abstract: 

    In this work, chicken HPAIV H5N1 epitope-specific TCRαβ (ch-TCRαβ) was isolated and its structure was determined. The Cα domain of ch-TCRαβ does not exhibit the typical structure of human TCRαβ, and the DE loop extends outward, resulting in close proximity between the Cα domain of ch-TCRαβ and CD3εδ/γ. The FG loop of the Cβ domain of ch-TCRαβ is shorter. The changes in the C domains of ch-TCRαβ and the difference in chicken CD3εδ/γ confirm that the complexes formed by TCRαβ and CD3εδ/γ differ from those in humans. In the chicken complex, a positively charged cleft is formed between the two CDR3 loops that might accommodate the acidic side chains of the chicken pMHC-I-bound HPAIV epitope intermediate portion oriented toward ch-TCRαβ. This is the first reported structure of chicken TCRαβ, and it provides a structural model of the ancestral TCR system in the immune synapses between T cells and antigen-presenting cells in lower vertebrates.


  • Organizational Affiliation

    Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing 100193, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TCR alpha chain
A, C
218Gallus gallusMutation(s): 0 
Gene Names: TCR alpha chain
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TCR beta chain
B, D
239Gallus gallusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.43α = 90
b = 83.097β = 117.716
c = 82.416γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-18
    Type: Initial release
  • Version 1.1: 2021-03-17
    Changes: Database references