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5SWZ

H2-Db presenting "ASNENMETM" to Alpha/Beta T cell receptor 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.

Information sections


Complex type

Class i with peptide and alpha beta tcr

1. Beta 2 microglobulin
['B', 'G', 'L', 'Q']
2. Class I alpha
H2-Db
['A', 'F', 'K', 'P']
3. Peptide
ASNENMETM
['C', 'H', 'M', 'R']
4. T cell receptor alpha
TRAV14
['D']
5. T cell receptor beta
TRBV17
['E']

Species


Locus / Allele group


Publication

Reversed T Cell Receptor Docking on a Major Histocompatibility Class I Complex Limits Involvement in the Immune Response.

Gras S, Chadderton J, Del Campo CM, Farenc C, Wiede F, Josephs TM, Sng XYX, Mirams M, Watson KA, Tiganis T, Quinn KM, Rossjohn J, La Gruta NL
Immunity (2016) 45, 749-760 [doi:10.1016/j.immuni.2016.09.007]  [pubmed:27717799

The anti-viral T cell response is drawn from the naive T cell repertoire. During influenza infection, the CD8+ T cell response to an H-2Db-restricted nucleoprotein epitope (NP366) is characterized by preferential expansion of T cells bearing TRBV13+ T cell receptors (TCRs) and avoidance of TRBV17+ T cells, despite the latter dominating the naive precursor repertoire. We found two TRBV17+ TCRs that bound H-2Db-NP366 with a 180° reversed polarity compared to the canonical TCR-pMHC-I docking. The TRBV17 β-chain dominated the interaction and, whereas the complementarity determining region-3 (CDR3) loops exclusively mediated contacts with the MHC-I, peptide specificity was attributable to germline-encoded recognition. Nevertheless, the TRBV17+ TCR exhibited moderate affinity toward H-2Db-NP366 and was capable of signal transduction. Thus, the naive CD8+ T cell pool can comprise TCRs adopting reversed pMHC-I docking modes that limit their involvement in the immune response.

Structure deposition and release

Deposited: 2016-08-09
Released: 2016-10-05
Revised: 2016-10-26

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: ASNENMETM

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 ALA

GLU163
GLU63
TRP167
MET5
TYR171
TYR7
LYS66
TYR159
TYR59
P2 SER

TYR45
GLU163
GLU63
TYR7
LYS66
TYR159
P3 ASN

GLU9
LYS66
GLN70
TYR159
TYR156
LEU114
P4 GLU

LYS66
TYR156
GLY69
GLN65
GLN70
P5 ASN

PHE74
GLU9
PHE116
TYR156
GLN97
GLN70
TRP73
P6 MET

HIS155
ALA152
TYR156
TRP73
P7 GLU

TYR156
SER150
TRP73
LYS146
TRP147
P8 THR

VAL76
TRP147
TRP73
LYS146
SER77
ASN80
P9 MET

THR143
PHE116
SER77
TYR84
LEU95
TYR123
LYS146
ILE124
TRP147
TRP73
LEU81
ASN80

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
FQKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRWEPPPST

3. Peptide
ASNENMETM

4. T cell receptor alpha
T cell receptor alpha
TRAV14
        10        20        30        40        50        60
QQQVRQSPQSLTVWEGETAILNCSYEDSTFNYFPWYQQFPGEGPALLISIRSVSDKKEDG
        70        80        90       100       110       120
RFTIFFNKREKKLSLHITDSQPGDSATYFCAASETSGSWQLIFGSGTTVSVSPNIQNPDP
       130       140       150       160       170       180
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
       190       200
KSDFACANAFNNSIIPEDTFFPSPESS

5. T cell receptor beta
T cell receptor beta
TRBV17
        10        20        30        40        50        60
DTTVKQNPRYKLARVGKPVNLICSQTMNHDTMYWYQKKPNQAPKLLLFYYDKILNREADT
        70        80        90       100       110       120
FEKFQSSRPNNSFCSLYIGSAGLEYSAMYLCASSRDLGRDTQYFGPGTRLTVLEDLKNVF
       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]
  1. 5SWZ assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 5SWZ assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 5SWZ assembly 1  
Peptide only [cif]
  1. 5SWZ assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/5swz

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