8D5Q | pdb_00008d5q

TCR TG6 in complex with Ld-HF10

• PDB DOI: https://doi.org/10.2210/pdb8D5Q/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Toxoplasma gondii
• Expression System: Escherichia coli, Trichoplusia ni
• Mutation(s): No 


• Deposited: 2022-06-05 Released: 2022-09-14 
• Deposition Author(s): Wang, Y., Dai, S.
• Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.174 (DCC) 

Starting Models: experimental

Literature

Peptide Centric V beta Specific Germline Contacts Shape a Specialist T Cell Response.

Wang, Y., Tsitsiklis, A., Devoe, S., Gao, W., Chu, H.H., Zhang, Y., Li, W., Wong, W.K., Deane, C.M., Neau, D., Slansky, J.E., Thomas, P.G., Robey, E.A., Dai, S.

(2022) Front Immunol 13: 847092-847092

• PubMed: 35967379 
• DOI: https://doi.org/10.3389/fimmu.2022.847092
• Primary Citation Related Structures: 
  8D5N, 8D5P, 8D5Q


• PubMed Abstract: 
  

  Certain CD8 T cell responses are particularly effective at controlling infection, as exemplified by elite control of HIV in individuals harboring HLA-B57. To understand the structural features that contribute to CD8 T cell elite control, we focused on a strongly protective CD8 T cell response directed against a parasite-derived peptide (HF10) presented by an atypical MHC-I molecule, H-2Ld. This response exhibits a focused TCR repertoire dominated by Vβ2, and a representative TCR (TG6) in complex with Ld-HF10 reveals an unusual structure in which both MHC and TCR contribute extensively to peptide specificity, along with a parallel footprint of TCR on its pMHC ligand. The parallel footprint is a common feature of Vβ2-containing TCRs and correlates with an unusual Vα-Vβ interface, CDR loop conformations, and Vβ2-specific germline contacts with peptides. Vβ2 and Ld may represent "specialist" components for antigen recognition that allows for particularly strong and focused T cell responses.

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Organizational Affiliation: 
• Department of Pharmaceutical Sciences, University of Colorado School of Pharmacy, Aurora, CO, United States.
Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States.
Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States.
Biological Physics Laboratory, College of Science, Beijing Forestry University, Beijing, China.
Department of Statistics, University of Oxford, Oxford, United Kingdom.
Department of Chemistry and Chemical Biology, Northeastern Collaborative Access Team (NE-CAT), Advanced Photon Source, Argonne National Laboratory, Cornell University, Argonne, IL, United States.
Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 73.73 kDa 
• Atom Count: 5,349 
• Modeled Residue Count: 635 
• Deposited Residue Count: 643 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TCR-alpha	A	209	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TCR-beta	B	244	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class I histocompatibility antigen, L-D alpha chain	C	180	Mus musculus	Mutation(s): 0  Gene Names: H2-L
UniProt
Find proteins for P01897 (Mus musculus) Explore P01897  Go to UniProtKB:  P01897

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Dense granule protein 6, HF10 peptide	D [auth E]	10	Toxoplasma gondii	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	F [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4	E [auth B], G [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.174 (DCC) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.963	α = 90
b = 89.963	β = 90
c = 105.982	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-09-14 
Deposition Author(s): Wang, Y., Dai, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	--

Revision History  

• Version 1.0: 2022-09-14
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary