7TLT

HLA-A*29:02 binding "YFPLQSYGF" at 2.30Å 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', 'D']

2. Class I alpha
HLA-A*29:02

['A', 'C']

3. Peptide
YFPLQSYGF

['E', 'F']

Species

Homo sapiens (Human)

Locus / Allele group

HLA-A / HLA-A*29

Publication

SARS-CoV-2 Spike-derived peptide S489-497 (YFPLQSYGF) presented by HLA-A*29:02

Murdolo, L.D., Szeto, C., Gras, S.

Structure deposition and release

Deposited: 2022-01-18

Released: 2022-10-12

Revised: 2022-10-12

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: YFPLQSYGF

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 TYR

PHE33

MET5

TYR59

TYR7

LEU62

ASN66

TYR171

THR163

TRP167

GLN63

TYR99

P2 PHE

ASN66

THR9

GLN63

MET45

TYR99

VAL67

MET97

GLN70

TYR7

P3 PRO

TYR159

ASN66

THR163

GLN63

TYR99

P4 LEU

ALA69

TYR159

ARG65

ASN66

P5 GLN

GLN70

TYR159

LEU156

ARG114

TYR99

MET97

P6 SER

ALA69

GLN70

ASN66

THR73

P7 TYR

TRP147

GLN155

ASN77

TYR159

LEU156

THR73

ARG114

VAL152

P8 GLY

THR143

LYS146

ASN77

THR73

TRP147

P9 PHE

TRP147

TYR123

ILE142

THR143

LYS146

ASP116

LEU81

ILE124

ILE95

THR80

TYR84

ASN77

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

ALA159

ALA163

THR167

TRP171

ALA5

ARG59

ASP63

SER66

ARG7

B Pocket

ALA24

THR34

ARG45

ASP63

SER66

GLN67

ARG7

GLU70

LEU9

ARG99

C Pocket

GLU70

ALA73

PRO74

LEU9

THR97

D Pocket

ALA114

ARG155

SER156

ALA159

ALA160

ARG99

E Pocket

ALA114

TYR147

GLU152

SER156

THR97

F Pocket

SER116

TYR123

ASP143

ASP146

TYR147

GLU77

GLY80

PRO81

TRP84

SER95

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 MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD 70 80 90 WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

2. Class I alpha HLA-A29:02 IPD-IMGT/HLA* [ipd-imgt:HLA32485]	10 20 30 40 50 60 MAVMAPRTLLLLLLGALALTQTWAGSHSMRYFTTSVSRPGRGEPRFIAVGYVDDTQFVRF 70 80 90 100 110 120 DSDAASQRMEPRAPWIEQEGPEYWDLQTRNVKAQSQTDRANLGTLRGYYNQSEAGSHTIQ 130 140 150 160 170 180 MMYGCDVGSDGRFLRGYRQDAYDGKDYIALNEDLRSWTAADMAAQITQRKWEAARVAEQL 190 200 210 220 230 240 RAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLT 250 260 270 280 290 300 WQRDGEDQTQDTELVETRPAGDGTFQKWASVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP 310 320 330 340 350 360 SSQPTIPIVGIIAGLVLFGAVFAGAVVAAVRWRRKSSDRKGGSYSQAASSDSAQGSDMSL TACKV

3. Peptide	YFPLQSYGF

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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e.g. load http://www.histo.fyi/structures/downloads/1hhk_1_peptide.cif

or in the case of JSON formatted files to retrieve it and use it as part of notebooks such as Jupyter or GoogleColab.

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/7tlt

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.