6A6H

SLA-2*04:02 binding "MTAHIVVPY" at 2.31Å 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.

Complex type

Class i with peptide

1. Beta 2 microglobulin

['B']

2. Class I alpha
SLA-2*04:02

['A']

3. Peptide
MTAHIVVPY

['C']

Species

Sus scrofa (Feral Pig)

Locus / Allele group

SLA-2 / SLA-2*04

Publication

Crystallization of SLA-2*04:02:02 complexed with a CTL epitope derived from FMDV.

Ning S, Wang ZB, Qi P, Xiao J, Wang XJ

Res. Vet. Sci. (2019) 128, 90-98 [doi:10.1016/j.rvsc.2019.11.002] [pubmed:31760318]

Presentation of viral epitopes by swine MHC I (termed leukocyte antigen class I, SLA I) to cytotoxic T lymphocytes (CTLs) is crucial for swine immunity. The SLA-2 structure, however, remains largely unknown. To illustrate the structural basis of swine CTL epitope presentation, the crystal structure of SLA-2*04:02:02 complexed with one peptide, derived from foot-and-mouth disease virus (FMDV), was analyzed in this study. SLA-2*04:02:02 and swine β2-microglobulin (sβ2m) were refolded in vitro in the presence of peptides. X-ray diffraction data of SLA-2*04:02:02-peptide-sβ2m (referred to as p/SLA-2*04:02:02) were collected. The diffraction dataset was 2.3 Å in resolution and the space group was P3(2)21. Relevant data included a = 101.8 Å, b = 101.8 Å, c = 73.455 Å,α = 90.00°, β = 90.00°, γ = 120.00°. The structure of p/SLA-2*04:02:02 was analyzed. The results revealed that Glu24, Met68, Gly76, and Gln173 in PBG of SLA-2*04:02:02 are different from other MHC I. Furthermore, Asn63 is different from other SLA I. Gln57, Met174 and Gln180 in PBG of SLA I are different from other species' MHC I. All of these features are different from known mammalian peptide-MHC class I complexes (referred to as p/MHC I). In addition, P4-His, P6-Val, and P8-Pro in the peptide were exposed, and these residues as epitopes can be presented by SLA-2*04:02:02. This study not only provides a structural basis for peptide presentation by SLA-2, but also screens one potential FMDV CTL epitope. The results may be of interest in future vaccine development.

Structure deposition and release

Deposited: 2018-06-28

Released: 2019-07-03

Revised: 2020-01-15

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: MTAHIVVPY

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 MET

TYR159

ARG62

TRP167

TYR7

LEU5

TYR171

TYR59

ASN63

ASN66

PHE33

THR163

P2 THR

ASN63

ASN66

THR163

GLU24

TYR159

TYR7

ARG62

ALA67

MET45

TYR99

P3 ALA

TRP156

TYR99

ASN70

ASN66

TYR159

P4 HIS

ASN66

GLN155

P5 ILE

VAL152

TRP156

GLN155

TYR159

ILE73

ASN70

P6 VAL

GLN155

ILE73

ASN70

P7 VAL

GLN155

LYS146

ILE73

VAL152

TRP147

ALA150

P8 PRO

ASN77

ILE73

LYS146

P9 TYR

ALA81

LYS146

ASN77

ILE73

THR143

TYR84

TRP147

LEU95

THR80

TYR123

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

TYR159

THR163

TRP167

TYR171

LEU5

TYR59

ASN63

ASN66

TYR7

B Pocket

GLU24

VAL34

MET45

ASN63

ASN66

ALA67

TYR7

ASN70

ASP9

TYR99

C Pocket

ASN70

ILE73

TYR74

ASP9

ILE97

D Pocket

SER114

GLN155

TRP156

TYR159

LEU160

TYR99

E Pocket

SER114

TRP147

VAL152

TRP156

ILE97

F Pocket

ASP116

TYR123

THR143

LYS146

TRP147

ASN77

THR80

ALA81

TYR84

LEU95

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 VARPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSFSKDWS 70 80 90 FYLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWDRDH

2. Class I alpha SLA-204:02 IPD-MHC* [ipd-mhc:SLA06150]	10 20 30 40 50 60 GPHSLRYFDTAVSRPDRGEPRFIEVGYVDDTQFVRFDSDAPNPRMEPRAPWIQQEGQEYW 70 80 90 100 110 120 DRNTRNAMGNAQIYRGNLRTALGYYNQSEAGSHTLQIMYGCDVGPDGLLLRGYSQDAYDG 130 140 150 160 170 180 ADYIALNEDLRSWTAADTAAQITKRKWEAANVAEQWRSYLQGTCVEWLQKYLQMGKDTLQ 190 200 210 220 230 240 RAEPPKTHVTRHPSSDLGVTLRCWALGFYPKEISLTWQREGQDQSQDMELVETRPSGDGT 250 260 270 FQKWAALVVPPGEEQSYTCHVQHEGLQEPLTLRWD

3. Peptide	MTAHIVVPY

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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Complete structures

Aligned structures [cif]

6A6H assembly 1

Components

MHC Class I alpha chain [cif]

6A6H assembly 1

MHC Class I antigen binding domain (alpha1/alpha2) [cif]

6A6H assembly 1

Peptide only [cif]

6A6H assembly 1

Derived data

Data for this page [json]

https://api.histo.fyi/v1/structures/6a6h

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

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.