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7N5Q

H2-Db binding "SSLCNFRAYV" at 1.76Å 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.

Information sections


Complex type

Class i with peptide

1. Beta 2 microglobulin
['B', 'G']
2. Class I alpha
H2-Db
['A', 'F']
3. Peptide
SSLCNFRAYV
['C', 'H']

Species


Locus / Allele group


Publication

Covalent TCR-peptide-MHC interactions induce T cell activation and redirect T cell fate in the thymus.

Szeto C, Zareie P, Wirasinha RC, Zhang JB, Nguyen AT, Riboldi-Tunnicliffe A, La Gruta NL, Gras S, Daley SR
Nat Commun (2022) 13, 4951 [doi:10.1038/s41467-022-32692-4]  [pubmed:35999236

Interactions between a T cell receptor (TCR) and a peptide-major histocompatibility complex (pMHC) ligand are typically mediated by noncovalent bonds. By studying T cells expressing natural or engineered TCRs, here we describe covalent TCR-pMHC interactions that involve a cysteine-cysteine disulfide bond between the TCR and the peptide. By introducing cysteines into a known TCR-pMHC combination, we demonstrate that disulfide bond formation does not require structural rearrangement of the TCR or the peptide. We further show these disulfide bonds still form even when the initial affinity of the TCR-pMHC interaction is low. Accordingly, TCR-peptide disulfide bonds facilitate T cell activation by pMHC ligands with a wide spectrum of affinities for the TCR. Physiologically, this mechanism induces strong Zap70-dependent TCR signaling, which triggers T cell deletion or agonist selection in the thymus cortex. Covalent TCR-pMHC interactions may thus underlie a physiological T cell activation mechanism that has applications in basic immunology and potentially in immunotherapy.

Structure deposition and release

Deposited: 2021-06-06
Released: 2022-07-20
Revised: 2022-08-31

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: SSLCNFRAYV

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 SER

LYS66
MET5
TRP167
TYR171
TYR159
TYR59
TYR7
GLU63
PHE33
GLU163
P10 VAL

TYR84
THR143
TYR123
TRP147
ASN80
PHE116
LEU81
LEU95
LYS146
SER77
TRP73
P2 SER

TYR7
GLU63
GLU163
LYS66
TYR45
TYR159
P3 LEU

TYR156
GLN97
SER99
TYR159
TYR7
GLU9
GLN70
HIS155
LYS66
LEU114
P4 CYS

GLN70
HIS155
LYS66
TYR156
P5 ASN

PHE116
GLN70
HIS155
TRP73
TYR156
GLN97
GLU9
PHE74
P6 PHE

SER150
TRP73
ALA152
TYR156
GLY151
HIS155
P7 ARG

SER150
TRP73
P8 ALA

TRP147
TYR156
LYS146
SER150
TRP73
P9 TYR

LYS146
SER77
GLN72
TRP73
THR143
TRP147
ASN80
VAL76

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

ILE24
PHE34
ARG45
ARG63
GLN66
LYS67
ARG7
GLY70
PHE9
MET99
C Pocket

GLY70
GLN73
TRP74
PHE9
GLN97
D Pocket

TYR114
GLU155
HIS156
ALA159
TYR160
MET99
E Pocket

TYR114
LYS147
GLY152
HIS156
GLN97
F Pocket

GLN116
ASP123
ILE143
ARG146
LYS147
VAL77
ARG80
ASN81
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. Beta 2 microglobulin
Beta 2 microglobulin
        10        20        30        40        50        60
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
        70        80        90
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

2. Class I alpha
H2-Db
        10        20        30        40        50        60
MGPHSMRYFETAVSRPGLEEPRYISVGYVDNKEFVRFDSDAENPRYEPRAPWMEQEGPEY
        70        80        90       100       110       120
WERETQKAKGQEQWFRVSLRNLLGYYNQSAGGSHTLQQMSGCDLGSDWRLLRGYLQFAYE
       130       140       150       160       170       180
GRDYIALNEDLKTWTAADMAAQITRRKWEQSGAAEHYKAYLEGECVEWLHRYLKNGNATL
       190       200       210       220       230       240
LRTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDG
       250       260       270       280
TFQKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRWEPPSTD

3. Peptide
SSLCNFRAYV


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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or in the case of JSON formatted files to retrieve it and use it as part of notebooks such as Jupyter or GoogleColab.
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]
  1. 7N5Q assembly 1  
  2. 7N5Q assembly 2  

Components

MHC Class I alpha chain [cif]
  1. 7N5Q assembly 1  
  2. 7N5Q assembly 2  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 7N5Q assembly 1  
  2. 7N5Q assembly 2  
Peptide only [cif]
  1. 7N5Q assembly 1  
  2. 7N5Q assembly 2  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/7n5q

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