Ptal-N*01:01 binding "DFQESADSFL" at 2.10Å resolution
Data provenance
Information sections
- Publication
- Peptide details
- Peptide neighbours
- Binding cleft pockets
- Chain sequences
- Downloadable data
- Data license
- Footnotes
Complex type
Ptal-N*01:01
DFQESADSFL
Species
Locus / Allele group
Peptide presentation by bat MHC class I provides new insight into the antiviral immunity of bats.
Bats harbor many zoonotic viruses, including highly pathogenic viruses of humans and other mammals, but they are typically asymptomatic in bats. To further understand the antiviral immunity of bats, we screened and identified a series of bat major histocompatibility complex (MHC) I Ptal-N*01:01-binding peptides derived from four different bat-borne viruses, i.e., Hendra virus (HeV), Ebola virus (EBOV), Middle East respiratory syndrome coronavirus (MERS-CoV), and H17N10 influenza-like virus. The structures of Ptal-N*01:01 display unusual peptide presentation features in that the bat-specific 3-amino acid (aa) insertion enables the tight "surface anchoring" of the P1-Asp in pocket A of bat MHC I. As the classical primary anchoring positions, the B and F pockets of Ptal-N*01:01 also show unconventional conformations, which contribute to unusual peptide motifs and distinct peptide presentation. Notably, the features of bat MHC I may be shared by MHC I from various marsupials. Our study sheds light on bat adaptive immunity and may benefit future vaccine development against bat-borne viruses of high impact on humans.
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
ASP
ARG65
TYR7
TYR62
TRP170
TYR102
ASN69
TYR162
ASN66
|
P10
LEU
THR146
ASN83
LEU119
ILE98
TYR87
TYR126
TYR77
GLY80
LYS149
VAL84
TRP150
THR76
|
P2
PHE
ASN69
ALA45
TYR162
ARG35
ASN66
PHE36
VAL25
VAL34
ALA24
TYR7
TYR9
ALA70
TYR102
|
P3
GLN
TYR102
TYR162
ASN69
ARG100
TYR155
ARG158
ASP159
TYR9
|
P4
GLU
ASN69
ARG158
|
P5
SER
ALA73
ASN69
ASP72
THR76
ARG158
|
P6
ALA
ARG158
|
P7
ASP
THR76
ASP72
|
P8
SER
GLN75
THR76
VAL79
|
P9
PHE
ALA153
THR146
TYR155
THR76
ARG158
LYS149
TRP150
|
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
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW 70 80 90 SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM |
2. Class I alpha
Ptal-N*01:01
|
10 20 30 40 50 60
GFHSLRYFYTAWSRPGSGEPRFVAVGYVDDTQFVRFDSDNASPRAEPRAPWMDLVEQQDP 70 80 90 100 110 120 QYWDRNTRNARDAAQTYRVGLDNVRGYYNQSEAGSHTIQRMYGCDVGPHGRLLRGYDQLA 130 140 150 160 170 180 YDGADYIALNEDLRSWTAADLAAQNTRRKWEEAGYAERDRAYLEGECVEWLLKHLENGRE 190 200 210 220 230 240 TLLRADPPKTHITHHPISDREVTLRCWALGFYPEEITLTWQHDGEDQTQEMELVETRPDG 250 260 270 NGAFQKWAALVVPSGEEQRYTCHVQHEGLPQPLTLRW |
3. Peptide
|
DFQESADSFL
|
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.