8D5Q

Truncated H2-Ld binding "HPGSVNEFDF" at 2.50Å resolution

Data provenance

Structure downloaded from PDB Europe using the Coordinate Server. Aligned to residues 1-180 of 1HHK2 using the CEALIGN3 function of PyMol4. Chain assigment using a Levenshtein distance5 method using data from the PDBe REST API6. Organism data from PDBe REST API. Data for both of these operations from the Molecules endpoint. Structure visualised with 3DMol7.

Complex type

Truncated class i with peptide

1. Class I alpha
H2-Ld

['C']

2. Peptide
HPGSVNEFDF

['E']

Species

Mus musculus (Mouse)

Locus / Allele group

H2-L / H2-Ld

Publication

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

Wang Y, Tsitsiklis A, Devoe S, Gao W, Chu HH, Zhang Y, Li W, Wong WK, Deane CM, Neau D, Slansky JE, Thomas PG, Robey EA, Dai S

Front Immunol (2022) 13, 847092 [doi:10.3389/fimmu.2022.847092] [pubmed:35967379]

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.

Structure deposition and release

Deposited: 2022-06-05

Released: 2022-09-14

Revised: 2022-09-14

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication

Peptide details

Length: Decamer (10 amino acids)

Sequence: HPGSVNEFDF

Interactive view

Cutaway side view (static)

Surface top view (static - coloured by atom property)

Cutaway top view (static)

Data provenance

MHC:peptide complexes are visualised using PyMol. The peptide is superimposed on a consistent cutaway slice of the MHC binding cleft (displayed as a grey mesh) which best indicates the binding pockets for the P1/P5/PC positions (side view - pockets A, E, F) and for the P2/P3/PC-2 positions (top view - pockets B, C, D). In some cases peptides will use a different pocket for a specific peptide position (atypical anchoring). On some structures the peptide may appear to sterically clash with a pocket. This is an artefact of picking a standardised slice of the cleft and overlaying the peptide.

Peptide neighbours

P1 HIS

GLU163

TRP167

TYR99

PHE33

MET5

TYR159

TYR59

TYR171

ARG62

TYR7

P10 PHE

ILE124

LEU81

THR80

TRP147

TYR84

PHE116

LEU95

ILE142

TRP73

TYR123

ASN77

LYS146

THR143

P2 PRO

ILE63

TYR159

GLU9

TYR99

ARG62

TYR59

TYR7

TYR45

GLU163

P3 GLY

VAL66

TRP97

TYR99

GLN70

GLU9

TYR159

P4 SER

GLN70

TYR155

ARG62

VAL66

TRP97

P5 VAL

TRP73

GLN70

TYR155

VAL66

GLY69

P6 ASN

TRP97

TRP73

GLN70

TYR155

TYR156

PHE116

P7 GLU

TYR155

P8 PHE

ALA152

TRP147

GLY151

TYR155

TRP73

ALA150

P9 ASP

TRP73

VAL76

ASN77

LYS146

TRP147

Colour key

Aromatic Hydrophobic Acidic Basic Neutral/polar

Data provenance

Neighbours are calculated by finding residues with atoms within 5Å of each other using BioPython Neighboursearch module. The list of neighbours is then sorted and filtered to inlcude only neighbours where between the peptide and the MHC Class I alpha chain.

Colours selected to match the YRB scheme. [https://www.frontiersin.org/articles/10.3389/fmolb.2015.00056/full]

Binding cleft pockets

Peptide sidechain binding pockets (static)

Peptide terminii and backbone binding residues (static)

A Pocket

ALA159

GLY163

GLU167

ARG171

SER5

GLU59

ARG63

GLN66

ARG7

B Pocket

THR24

PHE34

ARG45

ARG63

GLN66

VAL67

ARG7

GLY70

TYR9

MET99

C Pocket

GLY70

GLN73

TRP74

TYR9

GLN97

D Pocket

TYR114

GLU155

TYR156

ALA159

TYR160

MET99

E Pocket

TYR114

LYS147

GLY152

TYR156

GLN97

F Pocket

GLN116

ASP123

ILE143

ARG146

LYS147

VAL77

ARG80

THR81

GLY84

THR95

Colour key

Binds N-terminus Binds P1 backbone Binds P2 backbone Binds PC-1 backbone Binds C-terminus

Data provenance

N-/C-terminus and peptide backbone binding residues are assigned according to previously published information and pockets are assigned according to an adaptation of a previously published set of residues. All numbering is currently that of the 'canonical' structures of human and mouse MHC Class I molecules.

Chain sequences

1. Class I alpha H2-Ld	10 20 30 40 50 60 MGPHSMRYYETATSRRGLGEPRYTSVGYVDDKEFVRFDSDAENPRYEPQVPWMEQEGPEY 70 80 90 100 110 120 WERITQVAKGQEQWFRVNLRTLLGYYNQSAGGTHTLQWMYGCDVGSDGRLLRGYEQFAYD 130 140 150 160 170 GCDYIALNEDLRTWTAADMAAQITRRKWEQAGAAEYYRAYLEGECVEWLHRYLKNGNATL

2. Peptide	HPGSVNEFDF

Data provenance

Sequences are retrieved via the Uniprot method of the RSCB REST API. Sequences are then compared to those derived from the PDB file and matched against sequences retrieved from the IPD-IMGT/HLA database for human sequences, or the IPD-MHC database for other species. Mouse sequences are matched against FASTA files from Uniprot. Sequences for the mature extracellular protein (signal petide and cytoplasmic tail removed) are compared to identical length sequences from the datasources mentioned before using either exact matching or Levenshtein distance based matching.

Downloadable data

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Please take note of the data license. Using data from this site assumes that you have read and will comply with the license.

Complete structures

Aligned structures [cif]

8D5Q assembly 1

Components

MHC Class I alpha chain [cif]

8D5Q assembly 1

MHC Class I antigen binding domain (alpha1/alpha2) [cif]

8D5Q assembly 1

Peptide only [cif]

8D5Q assembly 1

Derived data

Data for this page [json]

https://api.histo.fyi/v1/structures/8d5q

Data license

The data above is made available under a Creative Commons CC-BY 4.0 license. This means you can copy, remix, transform, build upon and redistribute the material, but you must give appropriate credit, provide a link to the license, and indicate if changes were made.

If you use any data downloaded from this site in a publication, please cite 'https://www.histo.fyi/'. A preprint is in preparation.

Footnotes

Protein Data Bank Europe - Coordinate Server
1HHK - HLA-A*02:01 binding LLFGYPVYV at 2.5Å resolution - PDB entry for 1HHK
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. - PyMol CEALIGN Method - Publication
PyMol - PyMol.org/pymol
Levenshtein distance - Wikipedia entry
Protein Data Bank Europe REST API - Molecules endpoint
3Dmol.js: molecular visualization with WebGL - 3DMol.js - Publication
Protein Data Bank Europe REST API - Publication endpoint
PubMed Central Europe REST API - Articles endpoint

This work is licensed under a Creative Commons Attribution 4.0 International License.