HLA-A*24:02 presenting "RYPLTFGWCF" to Alpha/Beta T cell receptor at 2.68Å 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*24:02
RYPLTFGWCF
None
TRBV30
Species
Locus / Allele group
Conserved V��1 binding geometry in a setting of locus-disparate pHLA recognition by ��/����TCRs: insight into recognition of HIV peptides by TCR.
An essential step in the development of effective antiviral humoral responses is cytokine-triggered class switch recombination resulting in the production of antibodies of a specific isotype. Most viral and parasitic infections in mice induce predominantly IgG2a-specific antibody responses that are stimulated by interferon gamma (IFN-γ). However, in some mice deficient in IFN-γ, class switching to IgG2a antibodies is relatively unaffected, indicating that another signal(s) can be generated upon viral or parasitic infections that trigger this response. Here, we found that a single recessive locus, provisionally called IFN-γ-independent IgG2a (Igii), confers the ability to produce IFN-γ-independent production of IgG2a antibodies upon retroviral infection. The Igii locus was mapped to chromosome 9 and was found to function in the radiation-resistant compartment. Thus, our data implicate nonhematopoietic cells in activation of antiviral antibody responses in the absence of IFN-γ.IMPORTANCE Understanding the signals that stimulate antibody production and class switch recombination to specific antibody isotypes is crucial for the development of novel vaccines and adjuvants. While an interferon gamma-mediated switch to the IgG2a isotype upon viral infection in mice has been well established, this investigation reveals a noncanonical, interferon gamma-independent pathway for antiretroviral antibody production and IgG2a class switch recombination that is controlled by a single recessive locus. Furthermore, this study indicates that the radiation-resistant compartment can direct antiviral antibody responses, suggesting that detection of infection by nonhematopoietic cells is involved is stimulating adaptive immunity.
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
ARG
TYR159
TYR59
GLU63
LYS66
GLY167
MET5
TYR171
TYR7
ARG170
THR163
|
P10
PHE
LYS146
TRP147
ILE142
THR143
TYR84
TYR123
LEU95
ASN77
ILE80
TYR116
ALA81
|
P2
TYR
MET97
VAL67
SER9
HIS70
TYR7
ALA24
TYR159
PHE22
GLU63
LYS66
MET45
|
P3
PRO
MET97
GLN156
TYR7
PHE99
TYR159
LYS66
|
P4
LEU
TYR159
LYS66
GLN156
|
P5
THR
ALA69
THR73
LYS66
HIS70
GLN156
|
P6
PHE
VAL152
GLN156
GLN155
|
P7
GLY
VAL152
TRP147
ALA150
|
P8
TRP
TYR116
THR73
ASN77
PHE99
HIS114
VAL152
HIS70
TRP147
GLN156
MET97
|
P9
CYS
ASN77
THR73
GLU76
LYS146
TRP147
THR143
|
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
GLY167
TYR171
MET5
TYR59
GLU63
LYS66
TYR7
|
B Pocket
ALA24
VAL34
MET45
GLU63
LYS66
VAL67
TYR7
HIS70
SER9
PHE99
|
C Pocket
HIS70
THR73
ASP74
SER9
MET97
|
D Pocket
HIS114
GLN155
GLN156
TYR159
LEU160
PHE99
|
E Pocket
HIS114
TRP147
VAL152
GLN156
MET97
|
F Pocket
TYR116
TYR123
THR143
LYS146
TRP147
ASN77
ILE80
ALA81
TYR84
LEU95
|
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*24:02
IPD-IMGT/HLA
[ipd-imgt:HLA34790] |
10 20 30 40 50 60
GSHSMRYFSTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW 70 80 90 100 110 120 DEETGKVKAHSQTDRENLRIALRYYNQSEAGSHTLQMMFGCDVGSDGRFLRGYHQYAYDG 130 140 150 160 170 180 KDYIALKEDLRSWTAADMAAQITKRKWEAAHVAEQQRAYLEGTCVDGLRRYLENGKETLQ 190 200 210 220 230 240 RTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT 250 260 270 FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRW |
3. Peptide
|
RYPLTFGWCF
|
4. T cell receptor alpha
T cell receptor alpha
None
|
10 20 30 40 50 60
QKVTQAQSSVSMPVRKAVTLNCLYETSWWSYYIFWYKQLPSKEMIFLIRQGSDEQNAKSG 70 80 90 100 110 120 RYSVNFKKAAKSVALTISALQLEDSAKYFCALGELARSGGYQKVTFGTGTKLQVIPNIQN 130 140 150 160 170 180 PDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVA 190 200 WSNKSDFACANAFNNSIIPEDTFFPSP |
5. T cell receptor beta
T cell receptor beta
TRBV30
|
10 20 30 40 50 60
SQTIHQWPATLVQPVGSPLSLECTVEGTSNPNLYWYRQAAGRGLQLLFYSVGIGQISSEV 70 80 90 100 110 120 PQNLSASRPQDRQFILSSKKLLLSDSGFYLCAWSVSVGAGVPTIYFGEGSWLTVVEDLNK 130 140 150 160 170 180 VFPPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVCTDPQPLKE 190 200 210 220 230 240 QPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEA WGRAD |
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.