5WLG

H2-Db presenting "SQLLNAKYL" to Alpha/Beta T cell receptor at 2.10Å 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 and alpha beta tcr

1. Beta 2 microglobulin

['B', 'G']

2. Class I alpha
H2-Db

['A', 'F']

3. Peptide
SQLLNAKYL

['C', 'H']

4. T cell receptor alpha
TRAV8

['D']

5. T cell receptor beta
TRBV13

['E']

Information on this structure on STCRdab.

Species

Mus musculus (Mouse)

Locus / Allele group

H2-D / H2-Db

Publication

A T Cell Receptor Locus Harbors a Malaria-Specific Immune Response Gene.

Van Braeckel-Budimir N, Gras S, Ladell K, Josephs TM, Pewe L, Urban SL, Miners KL, Farenc C, Price DA, Rossjohn J, Harty JT

Immunity (2017) 47, 835-847.e4 [doi:10.1016/j.immuni.2017.10.013] [pubmed:29150238]

Immune response (Ir) genes, originally proposed by Baruj Benacerraf to explain differential antigen-specific responses in animal models, have become synonymous with the major histocompatibility complex (MHC). We discovered a non-MHC-linked Ir gene in a T cell receptor (TCR) locus that was required for CD8⁺ T cell responses to the Plasmodium berghei GAP50_40-48 epitope in mice expressing the MHC class I allele H-2D^b. GAP50_40-48-specific CD8⁺ T cell responses emerged from a very large pool of naive Vβ8.1⁺ precursors, which dictated susceptibility to cerebral malaria and conferred protection against recombinant Listeria monocytogenes infection. Structural analysis of a prototypical Vβ8.1⁺ TCR-H-2D^b-GAP50_40-48 ternary complex revealed that germline-encoded complementarity-determining region 1β residues present exclusively in the Vβ8.1 segment mediated essential interactions with the GAP50_40-48 peptide. Collectively, these findings demonstrated that Vβ8.1 functioned as an Ir gene that was indispensable for immune reactivity against the malaria GAP50_40-48 epitope.

Structure deposition and release

Deposited: 2017-07-26

Released: 2017-11-15

Revised: 2019-05-29

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: SQLLNAKYL

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 SER

ARG62

GLU63

TYR159

TYR171

TYR59

TYR7

LYS66

GLU163

TRP167

PHE33

MET5

P2 GLN

GLU163

TYR7

GLN70

GLU63

LYS66

GLU9

TYR45

SER24

TYR159

TYR22

ALA67

P3 LEU

SER99

TYR159

GLN70

LEU114

TYR156

HIS155

GLU9

GLN97

P4 LEU

GLN70

LYS66

TYR156

HIS155

GLY69

P5 ASN

GLN70

LEU114

TYR156

PHE116

HIS155

PHE74

TRP73

GLN97

P6 ALA

ALA152

TYR156

HIS155

TRP73

P7 LYS

ALA152

TYR156

LYS146

TRP73

TRP147

SER150

P8 TYR

SER77

THR143

GLN72

VAL76

LYS146

TRP73

ASN80

TRP147

P9 LEU

SER77

ASN80

LEU81

LEU95

THR143

TYR84

LYS146

ILE124

PHE116

TYR123

TRP147

TRP73

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 IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW 70 80 90 SFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM

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 FQKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRWEPPP

3. Peptide	SQLLNAKYL

4. T cell receptor alpha T cell receptor alpha TRAV8	10 20 30 40 50 60 ENLQALSIQEGEDVTMNCSYKTYTTVVHWYRQDSGRGPALIILIRSNEREKRSGRLRATL 70 80 90 100 110 120 DTSSQSSSLSITAAQCEDTAVYFCATVYAQGLTFGLGTRVSVFPNIQNPDPAVYQLRDSK 130 140 150 160 170 180 SSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANA FN

5. T cell receptor beta T cell receptor beta TRBV13	10 20 30 40 50 60 EAAVTQSPRSKVAVTGGKVTLSCHQTNNHDYMYWYRQDTGHGLRLIHYSYVADSTEKGDI 70 80 90 100 110 120 PDGYKASRPSQENFSLILELASLSQTAVYFCASSDWGDTGQLYFGEGSKLTVLEDLKNVF 130 140 150 160 170 180 PPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQP 190 200 210 220 230 240 ALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWG RAD

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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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]

5WLG assembly 1

Components

MHC Class I alpha chain [cif]

5WLG assembly 1

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

5WLG assembly 1

Peptide only [cif]

5WLG assembly 1

Derived data

Data for this page [json]

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

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.