8D5N | pdb_00008d5n

Crystal structure of Ld-HF10

PDB DOI: https://doi.org/10.2210/pdb8D5N/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus, Toxoplasma gondii
Expression System: Trichoplusia ni, Podospora comata
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 Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.219 (Depositor), 0.223 (DCC)
R-Value Work:
0.178 (Depositor), 0.186 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
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.

Organizational Affiliation

Department of Pharmaceutical Sciences, University of Colorado School of Pharmacy, Aurora, CO, United States.

Macromolecule Content

Total Structure Weight: 92.73 kDa
Atom Count: 6,715
Modeled Residue Count: 769
Deposited Residue Count: 804
Unique protein chains: 3

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class I histocompatibility antigen, L-D alpha chain	A [auth C], C [auth A]	282	Mus musculus	Mutation(s): 0 Gene Names: H2-L
UniProt
Find proteins for P01897 (Mus musculus) Explore P01897 Go to UniProtKB: P01897
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01897
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A [auth C] Focus chain C [auth A]	Go to GlyGen: P01897-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Dense granule protein 6, HF10 peptide	B [auth E], D [auth B]	16	Toxoplasma gondii	Mutation(s): 0 Gene Names: GRA6, TG24

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	E [auth F], F [auth H]	104	Mus musculus	Mutation(s): 0 Gene Names: B2m
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus) Explore P01887 Go to UniProtKB: P01887
IMPC: MGI:88127
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01887
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain G [auth C] MOL2 format, chain J [auth A] MOL2 format, chain G [auth C] mmCIF format, chain J [auth A] mmCIF format, chain G [auth C]	G [auth C], J [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth C] Focus chain J [auth A] Interactions & Density Focus chain G [auth C] Focus chain J [auth A]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain H [auth C] MOL2 format, chain H [auth C] mmCIF format, chain H [auth C]	H [auth C]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Interactions & Density Focus chain H [auth C]
PPI Query on PPI Download:Ideal Coordinates CCD File SDF format, chain I [auth E] MOL2 format, chain I [auth E] mmCIF format, chain I [auth E]	I [auth E]	PROPANOIC ACID C₃ H₆ O₂ XBDQKXXYIPTUBI-UHFFFAOYSA-N		Interactions Focus chain I [auth E] Interactions & Density Focus chain I [auth E]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain L [auth H] SDF format, chain K [auth F] MOL2 format, chain L [auth H] MOL2 format, chain K [auth F] mmCIF format, chain L [auth H] mmCIF format, chain K [auth F]	K [auth F], L [auth H]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain K [auth F] Focus chain L [auth H] Interactions & Density Focus chain K [auth F] Focus chain L [auth H]