HLA-A*02:01 presenting "ALGIGILTV" to Alpha/Beta T cell receptor at 2.88Å 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
HLA-A*02:01
ALGIGILTV
TRAV12
TRBV28
Species
Locus / Allele group
Structural description of how different MART-1 antigenic peptides influence JKF6 T cell receptor recognition
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
ALA
MET5
TYR159
PHE33
TYR59
THR163
GLU63
TYR7
TRP167
TYR171
LYS66
|
P2
LEU
TYR7
MET45
LYS66
TYR99
THR163
GLU63
HIS70
TYR159
VAL67
PHE9
|
P3
GLY
TYR159
TYR99
HIS70
LYS66
|
P4
ILE
LEU156
ALA158
GLN155
TYR159
|
P5
GLY
VAL152
GLN155
ARG97
LEU156
|
P6
ILE
TYR99
HIS114
THR73
HIS74
LEU156
ARG97
HIS70
|
P7
LEU
ASP77
TRP147
VAL152
LYS146
ARG97
THR73
ALA150
|
P8
THR
LYS146
VAL76
THR73
ASP77
TRP147
|
P9
VAL
TYR84
LEU81
LYS146
TYR116
THR143
TYR123
ASP77
TRP147
THR80
|
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
MET5
TYR59
GLU63
LYS66
TYR7
|
B Pocket
ALA24
VAL34
MET45
GLU63
LYS66
VAL67
TYR7
HIS70
PHE9
TYR99
|
C Pocket
HIS70
THR73
HIS74
PHE9
ARG97
|
D Pocket
HIS114
GLN155
LEU156
TYR159
LEU160
TYR99
|
E Pocket
HIS114
TRP147
VAL152
LEU156
ARG97
|
F Pocket
TYR116
TYR123
THR143
LYS146
TRP147
ASP77
THR80
LEU81
TYR84
VAL95
|
Colour key
Data provenance
1. Beta 2 microglobulin
Beta 2 microglobulin
|
10 20 30 40 50 60
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD 70 80 90 WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM |
2. Class I alpha
HLA-A*02:01
IPD-IMGT/HLA
[ipd-imgt:HLA35266] |
10 20 30 40 50 60
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW 70 80 90 100 110 120 DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG 130 140 150 160 170 180 KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ 190 200 210 220 230 240 RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT 250 260 270 FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE |
3. Peptide
|
ALGIGILTV
|
4. T cell receptor alpha
T cell receptor alpha
TRAV12
|
10 20 30 40 50 60
MQKEVEQNSGPLSVPEGAIASLNCTYSDRGSQSFFWYRQYSGKSPELIMSIYSNGDKEDG 70 80 90 100 110 120 RFTAQLNKASQYVSLLIRDAQPSDSATYLCAVSGGGADGLTFGKGTQVVVTPNIQNPDPA 130 140 150 160 170 180 VYQLRDSKSADKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNK 190 200 SDFACANAFNNSIIPEDTFFPSPESS |
5. T cell receptor beta
T cell receptor beta
TRBV28
|
10 20 30 40 50 60
MDKVTQSSRYLVKRTGEKVFLECVQDMDHENMFWYRQDPGLGLRLIYFSYDVKMKEKGDI 70 80 90 100 110 120 PEGYSVSREKKERFSLILASASTDQTSMYLCASSFLGTGVEQYFGPGTRLTVVEDLNKVF 130 140 150 160 170 180 PPEVALFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQP 190 200 210 220 230 240 ALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSEADEWTQDRAKPVTQIVSAEAWG RAD |
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.