H2-Kb presenting "WIYVYRPMGCGGS" to Alpha/Beta T cell receptor at 2.90Å resolution
Data provenance
Information sections
- Publication
- Peptide details
- Peptide neighbours
- Binding cleft pockets
- Chain sequences
- Downloadable data
- Data license
- Footnotes
Complex type
Class i with peptide and alpha beta tcr
H2-Kb
WIYVYRPMGCGGS
TRAV6
TRBV13
Species
Locus / Allele group
A single T cell receptor bound to major histocompatibility complex class I and class II glycoproteins reveals switchable TCR conformers.
Major histocompatibility complex class I (MHCI) and MHCII proteins differ in structure and sequence. To understand how T cell receptors (TCRs) can use the same set of variable regions to bind both proteins, we have presented a comparison of a single TCR bound to both MHCI and MHCII ligands. The TCR adopts similar orientations on both ligands with TCR amino acids thought to be evolutionarily conserved for MHC interaction occupying similar positions on the MHCI and MHCII helices. However, the TCR antigen-binding loops use different conformations when interacting with each ligand. Most importantly, we observed alternate TCR core conformations. When bound to MHCI, but not MHCII, Vα disengages from the Jα β strand, switching Vα's position relative to Vβ. In several other structures, either Vα or Vβ undergoes this same modification. Thus, both TCR V-domains can switch among alternate conformations, perhaps extending their ability to react with different MHC-peptide ligands.
Structure deposition and release
Data provenance
Publication data retrieved from PDBe REST API8 and PMCe REST API9
Other structures from this publication
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
TRP
THR163
GLU63
TRP167
LEU5
TYR159
ARG62
LYS66
TYR171
TYR59
TYR7
|
P10
CYS
LYS146
LEU81
ALA139
THR143
TYR123
ILE142
THR80
CYS84
|
P11
GLY
ALA139
MET138
ILE142
CYS84
ALA140
|
P12
GLY
TYR85
ALA139
MET138
ILE142
CYS84
|
P13
SER
ASP137
TYR85
ALA139
MET138
CYS84
|
P2
ILE
TYR159
LYS66
ASN70
VAL9
TYR45
TYR7
GLU24
GLU63
ALA67
|
P3
TYR
ARG155
ASN70
TYR159
LEU156
LYS66
GLN114
GLU152
|
P4
VAL
ARG155
ASN70
LYS66
|
P5
TYR
ARG155
PHE74
TYR116
SER73
VAL97
GLN114
ASN70
VAL9
GLU24
TYR22
TYR7
SER99
|
P6
ARG
GLU152
TRP147
ALA150
ARG155
TYR116
ASP77
|
P7
PRO
TRP147
SER73
ASP77
|
P8
MET
LYS146
PHE74
TYR116
LEU81
ILE95
ASP77
TRP147
THR143
TYR123
|
P9
GLY
ASP77
THR143
ILE142
THR80
LYS146
|
Colour key
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]
A Pocket
TYR159
THR163
TRP167
TYR171
LEU5
TYR59
GLU63
LYS66
TYR7
|
B Pocket
GLU24
VAL34
TYR45
GLU63
LYS66
ALA67
TYR7
ASN70
VAL9
SER99
|
C Pocket
ASN70
SER73
PHE74
VAL9
VAL97
|
D Pocket
GLN114
ARG155
LEU156
TYR159
LEU160
SER99
|
E Pocket
GLN114
TRP147
GLU152
LEU156
VAL97
|
F Pocket
TYR116
TYR123
THR143
LYS146
TRP147
ASP77
THR80
LEU81
CYS84
ILE95
|
Colour key
Data provenance
1. Beta 2 microglobulin
Beta 2 microglobulin
|
10 20 30 40 50 60
GIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKD 70 80 90 WSFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM |
2. Class I alpha
H2-Kb
|
10 20 30 40 50 60
GPHSLRYFVTAVSRPGLGEPRYMEVGYVDDTEFVRFDSDAENPRYEPRARWMEQEGPEYW 70 80 90 100 110 120 ERETQKAKGNEQSFRVDLRTLLGCYNQSKGGSHTIQVISGCEVGSDGRLLRGYQQYAYDG 130 140 150 160 170 180 SDYIALNEDLKTWTAADMAALITKHKWEQAGEAERLRAYLEGTCVEWLRRYLKNGNATLL 190 200 210 220 230 240 RTDSPKAHVTHHSRPEDKVTLRCWALGFYPADITLTWQLNGEELIQDMELVETRPAGDGT 250 260 270 FQKWASVVVPLGKEQYYTCHVYHQGLPEPLTLRWE |
3. Peptide
|
WIYVYRPMGCGGS
|
4. T cell receptor alpha
T cell receptor alpha
TRAV6
|
10 20 30 40 50 60
DSVTQMQGQVTLSENDFLFINCTYSTTGYPTLFWYVQYSGEGPQLLLQVTTANNKGSSRG 70 80 90 100 110 120 FEATYDKGTTSFHLQKTSVQEIDSAVYYCAANSGTYQRFGTGTKLQVVPNIQNPDPAVYQ 130 140 150 160 170 180 LRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDF 190 ACANAFNNSIIPEDTFFPSP |
5. T cell receptor beta
T cell receptor beta
TRBV13
|
10 20 30 40 50 60
AVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPD 70 80 90 100 110 120 GYKASRPSQENFSLILELATPSQTSVYFCASGDFWGDTLYFGAGTRLSVLEDLKNVFPPE 130 140 150 160 170 180 VAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALN 190 200 210 220 230 DSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAW |
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
Components
Data license
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.