Ptal-N*01:01 binding "DFEKEGYSL" at 2.30Å 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
DFEKEGYSL
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
TRP170
ASN69
TYR62
TYR162
ASN66
|
P2
PHE
TYR7
ALA24
VAL25
ASN66
ALA45
ALA70
TYR162
ARG35
PHE36
ASN69
TYR9
TYR102
VAL34
|
P3
GLU
ASN69
TYR9
TYR102
ARG100
ARG158
TYR162
ASP159
TYR155
|
P4
LYS
ASN69
|
P5
GLU
ARG158
TYR155
|
P6
GLY
TYR155
THR76
|
P7
TYR
TRP150
ALA153
TYR155
THR76
LYS149
|
P8
SER
VAL79
ASN83
GLY80
THR76
LYS149
TRP150
|
P9
LEU
ASN145
LYS149
TRP150
VAL84
ILE98
ILE127
THR146
ASN83
LEU119
TYR126
TYR77
GLY80
TYR87
|
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
GSHGFHSLRYFYTAWSRPGSGEPRFVAVGYVDDTQFVRFDSDNASPRAEPRAPWMDLVEQ 70 80 90 100 110 120 QDPQYWDRNTRNARDAAQTYRVGLDNVRGYYNQSEAGSHTIQRMYGCDVGPHGRLLRGYD 130 140 150 160 170 180 QLAYDGADYIALNEDLRSWTAADLAAQNTRRKWEEAGYAERDRAYLEGECVEWLLKHLEN 190 200 210 220 230 240 GRETLLRADPPKTHITHHPISDREVTLRCWALGFYPEEITLTWQHDGEDQTQEMELVETR 250 260 270 PDGNGAFQKWAALVVPSGEEQRYTCHVQHEGLPQPLTLRW |
3. Peptide
|
DFEKEGYSL
|
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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