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5NQ2

SLA-2*11:04 binding "IAYERMCNI" at 1.54Å resolution

Data provenance

Structure downloaded from PDB Europe using the Coordinate Server. Aligned to residues 1-180 of 1HHK2 using the CEALIGN3 function of PyMol4. Chain assigment using a Levenshtein distance5 method using data from the PDBe REST API6. Organism data from PDBe REST API. Data for both of these operations from the Molecules endpoint. Structure visualised with 3DMol7.

Information sections


Complex type

Class i with peptide

1. Beta 2 microglobulin
['B']
2. Class I alpha
SLA-2*11:04
['A']
3. Peptide
IAYERMCNI
['C']

Species


Locus / Allele group


Publication

Induction of influenza-specific local CD8 T-cells in the respiratory tract after aerosol delivery of vaccine antigen or virus in the Babraham inbred pig.

Tungatt K, Dolton G, Morgan SB, Attaf M, Fuller A, Whalley T, Hemmink JD, Porter E, Szomolay B, Montoya M, Hammond JA, Miles JJ, Cole DK, Townsend A, Bailey M, Rizkallah PJ, Charleston B, Tchilian E, Sewell AK
PLoS Pathog. (2018) 14, e1007017 [doi:10.1371/journal.ppat.1007017]  [pubmed:29772011

There is increasing evidence that induction of local immune responses is a key component of effective vaccines. For respiratory pathogens, for example tuberculosis and influenza, aerosol delivery is being actively explored as a method to administer vaccine antigens. Current animal models used to study respiratory pathogens suffer from anatomical disparity with humans. The pig is a natural and important host of influenza viruses and is physiologically more comparable to humans than other animal models in terms of size, respiratory tract biology and volume. It may also be an important vector in the birds to human infection cycle. A major drawback of the current pig model is the inability to analyze antigen-specific CD8+ T-cell responses, which are critical to respiratory immunity. Here we address this knowledge gap using an established in-bred pig model with a high degree of genetic identity between individuals, including the MHC (Swine Leukocyte Antigen (SLA)) locus. We developed a toolset that included long-term in vitro pig T-cell culture and cloning and identification of novel immunodominant influenza-derived T-cell epitopes. We also generated structures of the two SLA class I molecules found in these animals presenting the immunodominant epitopes. These structures allowed definition of the primary anchor points for epitopes in the SLA binding groove and established SLA binding motifs that were used to successfully predict other influenza-derived peptide sequences capable of stimulating T-cells. Peptide-SLA tetramers were constructed and used to track influenza-specific T-cells ex vivo in blood, the lungs and draining lymph nodes. Aerosol immunization with attenuated single cycle influenza viruses (S-FLU) induced large numbers of CD8+ T-cells specific for conserved NP peptides in the respiratory tract. Collectively, these data substantially increase the utility of pigs as an effective model for studying protective local cellular immunity against respiratory pathogens.

Structure deposition and release

Deposited: 2017-04-19
Released: 2018-04-25
Revised: 2019-05-08

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication


Peptide details

Length: Nonamer (9 amino acids)

Sequence: IAYERMCNI

Interactive view
Cutaway side view (static)
Surface top view (static - coloured by atom property)
Cutaway top view (static)

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 ILE

ARG63
CYS165
GLU167
GLY168
LEU6
GLU64
TYR172
TYR60
TYR160
TYR8
LEU164
P2 ALA

TYR160
TYR8
GLN68
ARG63
TYR100
TYR10
ILE67
GLU64
P3 TYR

GLN156
TRP157
TYR10
TYR160
ILE67
ASN71
TYR100
GLU153
P4 GLU

ARG63
TYR160
ILE67
LEU164
P5 ARG

ASP70
GLU153
THR74
P6 MET

TYR100
THR74
TRP157
PHE75
TYR10
SER98
TYR117
ASN71
P7 CYS

ASN78
GLU153
THR74
TRP148
P8 ASN

VAL77
THR74
LYS147
TRP148
ASN78
P9 ILE

TYR85
ASN78
ALA82
THR144
TYR124
THR81
LYS147
TRP148
PHE96

Colour key

Aromatic Hydrophobic Acidic Basic Neutral/polar

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]


Binding cleft pockets


Peptide sidechain binding pockets (static)
Peptide terminii and backbone binding residues (static)
A Pocket

SER159
GLY163
GLU167
ARG171
SER5
ASP59
ARG63
GLN66
SER7
B Pocket

ILE24
PHE34
ARG45
ARG63
GLN66
ILE67
SER7
ASP70
PHE9
MET99
C Pocket

ASP70
GLN73
THR74
PHE9
GLN97
D Pocket

TYR114
GLU155
GLN156
SER159
TYR160
MET99
E Pocket

TYR114
LYS147
ASP152
GLN156
GLN97
F Pocket

GLN116
ASP123
ILE143
ARG146
LYS147
VAL77
ARG80
THR81
GLY84
THR95

Colour key

Binds N-terminus Binds P1 backbone Binds P2 backbone Binds PC-1 backbone Binds C-terminus

Data provenance

N-/C-terminus and peptide backbone binding residues are assigned according to previously published information and pockets are assigned according to an adaptation of a previously published set of residues. All numbering is currently that of the 'canonical' structures of human and mouse MHC Class I molecules.

Chain sequences

1. Beta 2 microglobulin
Beta 2 microglobulin
        10        20        30        40        50        60
MMVARPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSFSKD
        70        80        90
WSFYLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWDRDH

2. Class I alpha
SLA-2*11:04
        10        20        30        40        50        60
MGPHSLSYFYTAVSRPDRGEPRFIAVGYVDDTQFVRFDSDAPNPRMEPRAPWIQQEGQDY
        70        80        90       100       110       120
WDRETQIQRDNAQTFRVNLRTALGYYNQSEAGSHTFQSMYGCYLGPDGLLLRGYSQYGYD
       130       140       150       160       170       180
SADYIALNEDLRSWTAADTAAQITKRKWEAADEAEQWRSYLQGLCVEGLRRYLEMGKDTL
       190       200       210       220       230       240
QRAEPPKTHVTRHPSSDLGVTLRCWALGFYPKEISLTWQREGQDQSQDMELVETRPSGDG
       250       260       270
TFQKWAALVVPPGEEQSYTCHVQHEGLQEPLTLRWDP

3. Peptide
IAYERMCNI


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

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Please take note of the data license. Using data from this site assumes that you have read and will comply with the license.

Complete structures

Aligned structures [cif]
  1. 5NQ2 assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 5NQ2 assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 5NQ2 assembly 1  
Peptide only [cif]
  1. 5NQ2 assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/5nq2

Data license

The data above is made available under a Creative Commons CC-BY 4.0 license. This means you can copy, remix, transform, build upon and redistribute the material, but you must give appropriate credit, provide a link to the license, and indicate if changes were made.
If you use any data downloaded from this site in a publication, please cite 'https://www.histo.fyi/'. A preprint is in preparation.

Footnotes