HLA-B*35:08 binding "CPSQEPMSIYVY" at 1.75Å resolution
Data provenance
Information sections
- Publication
- Peptide details
- Peptide neighbours
- Binding cleft pockets
- Chain sequences
- Downloadable data
- Data license
- Footnotes
Complex type
HLA-B*35:08
CPSQEPMSIYVY
Species
Locus / Allele group
Impact of clonal competition for peptide-MHC complexes on the CD8+ T-cell repertoire selection in a persistent viral infection.
CD8(+) T-cell responses to persistent viral infections are characterized by the accumulation of an oligoclonal T-cell repertoire and a reduction in the naive T-cell pool. However, the precise mechanism for this phenomenon remains elusive. Here we show that human cytomegalovirus (HCMV)-specific CD8(+) T cells recognizing distinct epitopes from the pp65 protein and restricted through an identical HLA class I allele (HLA B*3508) exhibited either a highly conserved public T-cell repertoire or a private, diverse T-cell response, which was uniquely altered in each donor following in vitro antigen exposure. Selection of a public T-cell receptor (TCR) was coincident with an atypical major histocompatibility complex (MHC)-peptide structure, in that the epitope adopted a helical conformation that bulged from the peptide-binding groove, while a diverse TCR profile was observed in response to the epitope that formed a flatter, more "featureless" landscape. Clonotypes with biased TCR usage demonstrated more efficient recognition of virus-infected cells, a greater CD8 dependency, and were more terminally differentiated in their phenotype when compared with the T cells expressing diverse TCR. These findings provide new insights into our understanding on how the biology of antigen presentation in addition to the structural features of the pMHC-I might shape the T-cell repertoire and its phenotype.
Structure deposition and release
Data provenance
Publication data retrieved from PDBe REST API8 and PMCe REST API9
Other structures from this publication
![](https://images.histo.fyi/cleft/side/combined/3bw9_1_combined_medium.png)
![](https://images.histo.fyi/cleft/yrb/3bw9_1_yrb_medium.png)
![](https://images.histo.fyi/cleft/top/combined/3bw9_1_combined_medium.png)
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
CYS
ARG62
PHE33
TYR171
TYR159
TYR7
TYR59
ASN63
MET5
TRP167
|
P10
TYR
THR73
TRP147
SER77
VAL152
GLN155
ARG156
ARG97
|
P11
VAL
LYS146
GLU76
THR73
TRP147
SER77
ASN80
|
P12
TYR
TRP147
SER77
ILE124
GLN96
TYR84
ILE95
TYR123
LYS146
ILE142
THR143
TYR74
SER116
ARG97
LEU81
ASN80
|
P2
PRO
TYR9
PHE67
TYR7
ILE66
TYR99
TYR159
ASN63
|
P3
SER
ASN70
TYR99
TYR159
TYR9
ILE66
ARG156
ARG97
|
P4
GLN
GLN65
THR69
ILE66
|
P5
GLU
TYR9
TYR99
ARG156
THR73
THR69
ARG97
ASN70
|
P6
PRO
THR73
THR69
|
P7
MET
GLN72
GLU76
THR73
THR69
|
P9
ILE
GLN155
TRP147
ALA150
VAL152
|
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]
![](https://images.histo.fyi/cleft/pockets/labelled/3bw9_1_labelled_medium.png)
![](https://images.histo.fyi/cleft/terminii/labelled/3bw9_1_labelled_medium.png)
A Pocket
TYR159
LEU163
TRP167
TYR171
MET5
TYR59
ASN63
ILE66
TYR7
|
B Pocket
ALA24
VAL34
THR45
ASN63
ILE66
PHE67
TYR7
ASN70
TYR9
TYR99
|
C Pocket
ASN70
THR73
TYR74
TYR9
ARG97
|
D Pocket
ASP114
GLN155
ARG156
TYR159
LEU160
TYR99
|
E Pocket
ASP114
TRP147
VAL152
ARG156
ARG97
|
F Pocket
SER116
TYR123
THR143
LYS146
TRP147
SER77
ASN80
LEU81
TYR84
ILE95
|
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-B*35:08
IPD-IMGT/HLA
[ipd-imgt:HLA31926] |
10 20 30 40 50 60
GSHSMRYFYTAMSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRTEPRAPWIEQEGPEYW 70 80 90 100 110 120 DRNTQIFKTNTQTYRESLRNLRGYYNQSEAGSHIIQRMYGCDLGPDGRLLRGHDQSAYDG 130 140 150 160 170 180 KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQRRAYLEGLCVEWLRRYLENGKETLQ 190 200 210 220 230 240 RADPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT 250 260 270 FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP |
3. Peptide
|
CPSQEPMSIYVY
|
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
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This work is licensed under a Creative Commons Attribution 4.0 International License.