Gaga-BF2*015:01 binding "RRREQTDY" at 2.71Å resolution
Data provenance
Information sections
- Publication
- Peptide details
- Peptide neighbours
- Binding cleft pockets
- Chain sequences
- Downloadable data
- Data license
- Footnotes
Complex type
Gaga-BF2*015:01
RRREQTDY
Species
Locus / Allele group
The Combination of CD8���� and Peptide-MHC-I in a Face-to-Face Mode Promotes Chicken ����T Cells Response.
The CD8αα homodimer is crucial to both thymic T cell selection and the antigen recognition of cytotoxic T cells. The CD8-pMHC-I interaction can enhance CTL immunity via stabilizing the TCR-pMHC-I interaction and optimizing the cross-reactivity and Ag sensitivity of CD8+ T cells at various stages of development. To date, only human and mouse CD8-pMHC-I complexes have been determined. Here, we resolved the pBF2*1501 complex and the cCD8αα/pBF2*1501 and cCD8αα/pBF2*0401 complexes in nonmammals for the first time. Remarkably, cCD8αα/pBF2*1501 and the cCD8αα/pBF2*0401 complex both exhibited two binding modes, including an "antibody-like" mode similar to that of the known mammal CD8/pMHC-I complexes and a "face-to-face" mode that has been observed only in chickens to date. Compared to the "antibody-like" mode, the "face-to-face" binding mode changes the binding orientation of the cCD8αα homodimer to pMHC-I, which might facilitate abundant γδT cells to bind diverse peptides presented by limited BF2 alleles in chicken. Moreover, the forces involving in the interaction of cCD8αα/pBF2*1501 and the cCD8αα/pBF2*0401 are different in this two binding model, which might change the strength of the CD8-pMHC-I interaction, amplifying T cell cross-reactivity in chickens. The coreceptor CD8αα of TCR has evolved two peptide-MHC-I binding patterns in chickens, which might enhance the T cell response to major or emerging pathogens, including chicken-derived pathogens that are relevant to human health, such as high-pathogenicity influenza viruses.
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
TYR171
THR163
LEU8
TYR61
TYR100
TYR159
GLU65
TYR10
TRP167
|
P2
ARG
TYR10
THR68
GLU65
VAL47
GLY29
HIS38
ALA46
SER69
TYR39
TRP62
TYR100
VAL28
THR37
TYR159
ASP27
|
P3
ARG
TYR100
SER114
TYR152
LEU98
THR68
LEU156
TYR159
THR72
|
P4
GLU
THR68
TYR152
ARG71
|
P5
GLN
TYR100
ILE75
ASP76
THR72
LEU98
TYR152
|
P6
THR
TRP147
TYR152
ILE75
|
P7
ASP
TRP147
ASP78
ILE75
LYS146
|
P8
TYR
TRP147
GLY79
PRO142
ARG86
VAL96
ASP116
LYS146
ILE75
THR82
PHE123
ASP76
THR143
LEU83
GLN97
LEU98
|
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]
1. Beta 2 microglobulin
Beta 2 microglobulin
|
10 20 30 40 50 60
DLTPKVQVYSRFPASAGTKNVLNCFAAGFHPPKISITLMKDGVPMEGAQYSDMSFNDDWT 70 80 90 FQRLVHADFTPSSGSTYACKVEHETLKEPQVYKWDPEF |
2. Class I alpha
Gaga-BF2*015:01
IPD-MHC
[ipd-mhc:CHICKEN08576] |
10 20 30 40 50 60
ELHTLRYISTAMTDPGPGQPWYVDVGYVDGELFTHYNSTARRAVPRTEWIAANTDQQYWD 70 80 90 100 110 120 SETQTSQRTEQIDRDGLGTLQRRYNQTGGSHTVQLMYGCDILEDGTIRGYSQDAYDGRDF 130 140 150 160 170 180 IAFDKDTMTFTAAVPEAVPTKRKWEEGDYAEGLKQYLEETCVEWLRRYVEYGKAELGRRE 190 200 210 220 230 240 RPEVRVWGKEADGILTLSCRAHGFYPRPIAVSWLKDGAVQGQDAQSGGIVPNGDGTYHTW 250 260 VTIDAQPGDGDKYQCRVEHASLPQPGLYSW |
3. Peptide
|
RRREQTDY
|
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.