1QLF

H2-Db binding "FAPSNYPAL" at 2.65Å 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
H2-Db

['A']

3. Peptide
FAPSNYPAL

['C']

Species

Mus musculus (Mouse)

Locus / Allele group

H2-D / H2-Db

Publication

Crystal structures of two H-2Db/glycopeptide complexes suggest a molecular basis for CTL cross-reactivity.

Glithero A, Tormo J, Haurum JS, Arsequell G, Valencia G, Edwards J, Springer S, Townsend A, Pao YL, Wormald M, Dwek RA, Jones EY, Elliott T

Immunity (1999) 10, 63-74 [doi:10.1016/s1074-7613(00)80007-2] [pubmed:10023771]

Two synthetic O-GlcNAc-bearing peptides that elicit H-2Db-restricted glycopeptide-specific cytotoxic T cells (CTL) have been shown to display nonreciprocal patterns of cross-reactivity. Here, we present the crystal structures of the H-2Db glycopeptide complexes to 2.85 A resolution or better. In both cases, the glycan is solvent exposed and available for direct recognition by the T cell receptor (TCR). We have modeled the complex formed between the MHC-glycopeptide complexes and their respective TCRs, showing that a single saccharide residue can be accommodated in the standard TCR-MHC geometry. The models also reveal a possible molecular basis for the observed cross-reactivity patterns of the CTL clones, which appear to be influenced by the length of the CDR3 loop and the nature of the immunizing ligand.

Structure deposition and release

Deposited: 1999-08-30

Released: 1999-09-01

Revised: 2020-07-29

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: FAPSNYPAL

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 PHE

PHE33

GLU63

MET5

TYR159

LYS66

TRP167

TYR171

TYR59

TYR7

GLU163

P2 ALA

GLU63

TYR45

TYR159

TYR7

LYS66

P3 PRO

LYS66

GLN97

GLN70

GLU9

TYR7

SER99

TYR159

P4 SER

TYR156

GLN70

LYS66

P5 ASN

GLN70

PHE116

TYR156

PHE74

TRP73

GLN97

P6 TYR

TYR156

HIS155

TRP73

ALA152

P7 PRO

TYR156

SER150

TRP147

TRP73

ALA152

P8 ALA

SER77

VAL76

LYS146

TRP147

TRP73

ASN80

P9 LEU

PHE116

SER77

THR143

TYR123

LEU95

LYS146

ILE124

TRP73

ASN80

TYR84

LEU81

TRP147

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

GLU163

TRP167

TYR171

MET5

TYR59

GLU63

LYS66

TYR7

B Pocket

SER24

VAL34

TYR45

GLU63

LYS66

ALA67

TYR7

GLN70

GLU9

SER99

C Pocket

GLN70

TRP73

PHE74

GLU9

GLN97

D Pocket

LEU114

HIS155

TYR156

TYR159

LEU160

SER99

E Pocket

LEU114

TRP147

ALA152

TYR156

GLN97

F Pocket

PHE116

TYR123

THR143

LYS146

TRP147

SER77

ASN80

LEU81

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 IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW 70 80 90 SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

2. Class I alpha H2-Db	10 20 30 40 50 60 GPHSMRYFETAVSRPGLEEPRYISVGYVDNKEFVRFDSDAENPRYEPRAPWMEQEGPEYW 70 80 90 100 110 120 ERETQKAKGQEQWFRVSLRNLLGYYNQSAGGSHTLQQMSGCDLGSDWRLLRGYLQFAYEG 130 140 150 160 170 180 RDYIALNEDLKTWTAADMAAQITRRKWEQSGAAEHYKAYLEGECVEWLHRYLKNGNATLL 190 200 210 220 230 240 RTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGT 250 260 270 FQKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRWEP

3. Peptide	FAPSNYPAL

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]

1QLF assembly 1

Components

MHC Class I alpha chain [cif]

1QLF assembly 1

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

1QLF assembly 1

Peptide only [cif]

1QLF assembly 1

Derived data

Data for this page [json]

https://api.histo.fyi/v1/structures/1qlf

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.