Gaga-BF2*002:01 binding "VIFPAKSL" at 3.13Å resolution
Data provenance
Information sections
- Publication
- Peptide details
- Peptide neighbours
- Binding cleft pockets
- Chain sequences
- Downloadable data
- Data license
- Footnotes
Complex type
Gaga-BF2*002:01
VIFPAKSL
Species
Locus / Allele group
Expression levels of MHC class I molecules are inversely correlated with promiscuity of peptide binding.
Highly polymorphic major histocompatibility complex (MHC) molecules are at the heart of adaptive immune responses, playing crucial roles in many kinds of disease and in vaccination. We report that breadth of peptide presentation and level of cell surface expression of class I molecules are inversely correlated in both chickens and humans. This relationship correlates with protective responses against infectious pathogens including Marek's disease virus leading to lethal tumours in chickens and human immunodeficiency virus infection progressing to AIDS in humans. We propose that differences in peptide binding repertoire define two groups of MHC class I molecules strategically evolved as generalists and specialists for different modes of pathogen resistance. We suggest that differences in cell surface expression level ensure the development of optimal peripheral T cell responses. The inverse relationship of peptide repertoire and expression is evidently a fundamental property of MHC molecules, with ramifications extending beyond immunology and medicine to evolutionary biology and conservation.
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
VAL
TYR7
TYR58
THR160
TRP164
TYR168
TYR156
GLN62
|
P2
ILE
GLY66
ILE65
TYR156
TYR7
GLN62
ASN69
TYR43
ASP24
TYR97
|
P3
PHE
ARG9
ASN69
TYR97
TYR149
ILE65
TYR156
GLY152
LEU153
TYR111
|
P4
PRO
ASN69
TYR149
ILE65
|
P5
ALA
ILE72
TYR149
ASN69
ASP73
ARG9
|
P6
LYS
LYS143
TRP144
GLY147
ASN76
ILE72
TYR149
|
P7
SER
TRP144
ASN76
ILE79
ILE72
LYS143
|
P8
LEU
ASN76
PRO139
ARG83
MET113
THR140
ILE79
PHE120
LYS143
LEU80
TRP144
|
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*002:01
IPD-MHC
[ipd-mhc:CHICKEN08567] |
10 20 30 40 50 60
ELHTLRYIRTAMTDPGPGLPWYVDVGYVDGELFVHYNSTARRYVPRTEWIAAKADQQYWD 70 80 90 100 110 120 GQTQIGQGNEQIDRENLGILQRRYNQTGGSHTVQWMYGCDILEGGPIRGYYQMAYDGRDF 130 140 150 160 170 180 TAFDKGTMTFTAAVPEAVPTKRKWEEGDYAEGLKQYLEETCVEWLRRYVEYGKAELGRRE 190 200 210 220 230 240 RPEVRVWGKEADGILTLSCRAHGFYPRPIVVSWLKDGAVRGQDAHSGGIVPNGDGTYHTW 250 260 270 280 290 300 VTIDAQPGDGDKYQCRVEHASLPQPGLYSWEPRSGGGLNDIFEAQKIEWHENSSSVDKLA AALEHHHHHH |
3. Peptide
|
VIFPAKSL
|
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
Complete structures
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.