6WL3

Truncated H2-Kb binding "RGYLYQGL" with pre TCR beta chain at 3.45Å 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

Truncated class i with peptide and pre tcr beta

1. Class I alpha
H2-Kb

['A', 'D', 'G']

2. Peptide
RGYLYQGL

['B', 'E', 'H']

3. pre T cell receptor beta

['C', 'F', 'I']

Species

Mus musculus (Mouse)

Locus / Allele group

H2-K / H2-Kb

Publication

Pre-T cell receptors topologically sample self-ligands during thymocyte ��-selection.

Li X, Mizsei R, Tan K, Mallis RJ, Duke-Cohan JS, Akitsu A, Tetteh PW, Dubey A, Hwang W, Wagner G, Lang MJ, Arthanari H, Wang JH, Reinherz EL

Science (2020) [doi:10.1126/science.abe0918] [pubmed:33335016]

Self-discrimination, a critical but ill-defined molecular process programmed during thymocyte development, requires myriad pre-T cell receptors (preTCRs) and αβTCRs. Using x-ray crystallography, we show how a preTCR applies the concave β-sheet surface of its single variable domain (Vβ) to "horizontally" grab the protruding MHC α2-helix. By contrast, αβTCRs purpose all six complementarity-determining region (CDR) loops of their paired VαVβ module to recognize peptides bound to major histocompatibility complex molecules (pMHCs) in "vertical" head-to-head binding. The preTCR topological fit ensures that CDR3β reaches the peptide's featured C-terminal segment for pMHC sampling, establishing the subsequent αβTCR canonical docking mode. "Horizontal" docking precludes germline CDR1β- and CDR2β-MHC binding to broaden β-chain repertoire diversification before αβTCR-mediated selection refinement. Thus, one subunit successively attunes the recognition logic of related multicomponent receptors.

Structure deposition and release

Deposited: 2020-04-18

Released: 2020-12-23

Revised: 2021-01-20

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication

Peptide details

Length: Octamer (8 amino acids)

Sequence: RGYLYQGL

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 ARG

TYR59

GLU63

TRP167

TYR7

LYS66

LEU5

TYR171

TYR45

TYR159

ARG62

THR163

P2 GLY

GLU63

TYR7

TYR159

LYS66

P3 TYR

ASN70

TYR159

ARG155

GLN114

SER99

LEU156

GLU152

LYS66

P4 LEU

ASN70

ARG155

GLU152

LYS66

P5 TYR

TYR116

VAL97

TYR7

SER73

ASN70

ARG155

GLN114

TYR22

SER99

GLU24

VAL9

PHE74

P6 GLN

GLU152

TYR116

SER73

ARG155

TRP147

P7 GLY

LYS146

ASP77

TRP147

SER73

P8 LEU

TYR116

LEU81

TYR123

ILE95

THR80

LYS146

THR143

ASP77

TRP147

TYR84

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

GLU63

LYS66

TYR7

B Pocket

GLU24

VAL34

TYR45

GLU63

LYS66

ALA67

TYR7

ASN70

VAL9

SER99

C Pocket

ASN70

SER73

PHE74

VAL9

VAL97

D Pocket

GLN114

ARG155

LEU156

TYR159

LEU160

SER99

E Pocket

GLN114

TRP147

GLU152

LEU156

VAL97

F Pocket

TYR116

TYR123

THR143

LYS146

TRP147

ASP77

THR80

LEU81

TYR84

ILE95

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. Class I alpha H2-Kb	10 20 30 40 50 60 GPHSLRYFVTAVSRPGLGEPRYMEVGYVDDTEFVRFDSDAENPRYEPRARWMEQECPEYW 70 80 90 100 110 120 ERETQKAKGNEQSFRVDLRTLLGYYNQSKGGSHTIQVISGCEVGSDGRLLRGYQQYAYDG 130 140 150 160 170 180 QDYIALNEDLKTWTAADMAALITKHKWEQAGEAERLRAYLEGTCVEWLRRYLKNGNATLL RTDSP

2. Peptide	RGYLYQGL

3. pre T cell receptor beta pre T cell receptor beta	10 20 30 40 50 60 DSGVVQSPRHIIKEKGGRSVLTCIPISGHSNVVWYQQTLGKELKFLIQHYEKVERDKGFL 70 80 90 100 110 120 PCRFSVQQFDDYHSEMNMSALELEDSAMYFCASSLRWGDEQYFGPGTRLTVVEDLRNVTP 130 140 150 160 170 180 PKVSLREPSKAEIANKQKATLQCQARGFFPDHVELSWWVNGKEVHSGVSTDPQAYKESNY 190 200 210 220 230 SYSLSSRLRVSATFWHNPRNHFRCQVQFHGLSEEDKWPEGSPKPVTQNISAEAWGRADS

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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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/6wl3

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.