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2E7L

Truncated H2-Ld presenting "QLSPFPFDL" to Alpha/Beta T cell receptor 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.

Information sections


Complex type

Truncated class i with peptide and alpha beta tcr

1. Class I alpha
H2-Ld
['E', 'F']
2. Peptide
QLSPFPFDL
['P', 'Q']
3. T cell receptor alpha
TRAV9
['A']
4. T cell receptor beta
TRBV13
['D']

Species


Locus / Allele group


Publication

How a single T cell receptor recognizes both self and foreign MHC.

Colf LA, Bankovich AJ, Hanick NA, Bowerman NA, Jones LL, Kranz DM, Garcia KC
Cell (2007) 129, 135-46 [doi:10.1016/j.cell.2007.01.048]  [pubmed:17418792

alphabeta T cell receptors (TCRs) can crossreact with both self- and foreign- major histocompatibility complex (MHC) proteins in an enigmatic phenomenon termed alloreactivity. Here we present the 2.35 A structure of the 2C TCR complexed with its foreign ligand H-2L(d)-QL9. Surprisingly, we find that this TCR utilizes a different strategy to engage the foreign pMHC in comparison to the manner in which it recognizes a self ligand H-2K(b)-dEV8. 2C engages both shared and polymorphic residues on L(d) and K(b), as well as the unrelated QL9 and dEV8 peptide antigens, in unique pair-wise contacts, resulting in greater structural complementarity with the L(d)-QL9 complex. In the structure of an engineered, high-affinity 2C TCR variant bound to H-2L(d)-QL9, the "wild-type" TCR-MHC binding orientation persists despite modified TCR-CDR3alpha interactions with peptide. Thus, a single TCR recognizes two globally similar, but distinct ligands by divergent mechanisms, indicating that receptor-ligand crossreactivity can occur in the absence of molecular mimicry.

Structure deposition and release

Deposited: 2007-01-11
Released: 2007-04-24
Revised: 2011-07-27

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication


Peptide details

Length: Nonamer (9 amino acids)

Sequence: QLSPFPFDL

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 GLN

ARG62
TYR59
TYR7
GLU163
TRP167
ILE63
MET5
TYR159
TYR171
P2 LEU

VAL66
TYR7
GLU163
ILE63
TYR45
TYR159
TYR99
P3 SER

GLU114
TYR99
GLN70
TYR159
TYR156
VAL66
ARG97
P4 PRO

GLN70
TYR159
TYR155
ARG97
P5 PHE

GLY69
TRP73
GLN70
TYR155
P6 PRO

GLN70
TYR156
PHE116
TYR155
TRP73
ARG97
P7 PHE

ASN77
ALA152
TRP147
TYR155
GLY151
TYR156
ALA150
TRP73
P8 ASP

TRP73
LYS146
THR143
ASN77
TRP147
P9 LEU

TRP147
THR80
TYR84
PHE116
LEU81
LEU95
TRP73
ILE142
TYR123
LYS146
THR143
ASN77

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

TYR159
GLU163
TRP167
TYR171
MET5
TYR59
ILE63
VAL66
TYR7
B Pocket

SER24
VAL34
TYR45
ILE63
VAL66
ALA67
TYR7
GLN70
GLU9
TYR99
C Pocket

GLN70
TRP73
PHE74
GLU9
ARG97
D Pocket

GLU114
TYR155
TYR156
TYR159
LEU160
TYR99
E Pocket

GLU114
TRP147
ALA152
TYR156
ARG97
F Pocket

PHE116
TYR123
THR143
LYS146
TRP147
ASN77
THR80
LEU81
TYR84
LEU95

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
GPHSMRYFETAVSRRGLGEPRYISVGYVDDKEFVRFDSDAENPRYEPQVPWMEQEGPEYW
        70        80        90       100       110       120
ERITQVAKGQEQWFRVNLRTLLGYYNQSAGGTHTLQRMYGCDVGSDGRLLRGYEQFAYDG
       130       140       150       160       170       180
CDYIALNEDLRTWTAADMAAQITRRKWEQAGAAEYYRAYLEGECVEWLHRYLKNGNATLL

R

2. Peptide
QLSPFPFDL

3. T cell receptor alpha
T cell receptor alpha
TRAV9
        10        20        30        40        50        60
QSVTQPDARVTVSEGASLQLRCKYSYSATPYLFWYVQYPRQGPQLLLKYYSGDPVVQGVN
        70        80        90       100       110
GFEAEFSKSNSSFHLRKASVHRSDSAVYFCAVSHQGRYLTFGSGTKVIVLPYN

4. T cell receptor beta
T cell receptor beta
TRBV13
        10        20        30        40        50        60
EAAVTQSPRNKVAVTGEKVTLSCNQTNNHNNMYWYRQDTGHELRLIYYSYGAGSTEKGDI
        70        80        90       100       110       120
PDGYKASRPSQENFSLTLESATPSQTSVYFCASGGGGTLYFGAGTRLSVLSSALEHHHHH

H


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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Complete structures

Aligned structures [cif]
  1. 2E7L assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 2E7L assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 2E7L assembly 1  
Peptide only [cif]
  1. 2E7L assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/2e7l

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