5H94

SLA-1*07:04 binding "KMNTQFTAV" at 1.48Å 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', 'E']

2. Class I alpha
SLA-1*07:04

['A', 'D']

3. Peptide
KMNTQFTAV

['C', 'F']

Species

Sus scrofa (Feral Pig)

Locus / Allele group

SLA-1 / SLA-1*07

Publication

Structural and biochemical analyses of swine MHC class I complexes and prediction of the epitope map in important influenza A strains.

Fan S, Wu Y, Wang S, Wang Z, Jiang B, Liu Y, Liang R, Zhou W, Zhang N, Xia C

J. Virol. (2016) [doi:10.1128/jvi.00119-16] [pubmed:27170754]

Almost simultaneously, several studies reported the emergence of novel SARS-CoV-2 lineages characterized by their phylogenetic and genetic distinction (1), (2), (3), (4).….

Structure deposition and release

Deposited: 2015-12-25

Released: 2016-05-18

Revised: 2017-10-04

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: KMNTQFTAV

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 LYS

GLU64

CYS165

SER168

TYR172

GLU171

LEU6

PHE34

LEU164

TYR60

TYR8

ARG63

TYR160

P2 MET

GLU46

ALA25

ARG63

TYR160

GLU64

SER68

TYR8

ASN71

ILE67

TYR100

TYR10

LEU164

P3 ASN

ILE67

GLU157

TYR100

ASN71

TYR10

HIS115

ARG63

TYR160

P4 THR

TRP153

ARG63

ILE67

GLU157

P5 GLN

ASN71

TYR10

HIS115

TYR100

TYR75

ASP70

TYR117

TRP153

THR74

ASN98

P6 PHE

ASP70

THR74

P7 THR

TRP153

ASN78

TRP148

THR74

SER151

P8 ALA

ASN78

TRP148

THR74

VAL77

ASN81

P9 VAL

LEU82

TYR124

ASN81

LYS147

ASN78

TRP148

PHE96

THR144

TYR85

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

LEU163

SER167

TYR171

LEU5

TYR59

GLU63

ILE66

TYR7

B Pocket

ALA24

VAL34

GLU45

GLU63

ILE66

SER67

TYR7

ASN70

TYR9

TYR99

C Pocket

ASN70

THR73

TYR74

TYR9

ASN97

D Pocket

HIS114

GLN155

GLU156

TYR159

LEU160

TYR99

E Pocket

HIS114

TRP147

TRP152

GLU156

ASN97

F Pocket

TYR116

TYR123

THR143

LYS146

TRP147

ASN77

ASN80

LEU81

TYR84

PHE95

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-107:04 IPD-MHC* [ipd-mhc:SLA08441]	10 20 30 40 50 60 GPHSLSYFYTAVSRPDRGDSRFIAVGYVDDTQFVRFDSDAPNPREEPRAPWIQQEGQEYW 70 80 90 100 110 120 DRETQISKDNAQTYRVNLNNLRGYYNQSEAGSHTFQNMYGCYLGPDGLLLHGYHQYAYDG 130 140 150 160 170 180 ADYIALNEDLRSWTAADTAAQITKRKWEASGWAEQERSYLQGLCVESLREYLEMGKDTLQ 190 200 210 220 230 240 RAEPPKTHVTRHPSSDLGVTLRCWALGFYPKEISLTWQREGQDQSQDMELVETRPSGDGT 250 260 270 FQKWAALVVPPGEEQSYTCHVQHEGLQEPLTLRWD

3. Peptide	KMNTQFTAV

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

Data can be downloaded to your local machine from the links below.

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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]

Components

MHC Class I alpha chain [cif]

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

Peptide only [cif]

Derived data

Data for this page [json]

https://api.histo.fyi/v1/structures/5h94

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.