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2NX5

HLA-B*35:01 presenting "EPLPQGQLTAY" to Alpha/Beta T cell receptor at 2.70Å 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', 'R']
2. Class I alpha
HLA-B*35:01
['A', 'F', 'K', 'Q']
3. Peptide
EPLPQGQLTAY
['C', 'H', 'M', 'S']
4. T cell receptor alpha
TRAV1
['D']
5. T cell receptor beta
TRBV10
['E']

Species


Locus / Allele group


Publication

A T cell receptor flattens a bulged antigenic peptide presented by a major histocompatibility complex class I molecule.

Tynan FE, Reid HH, Kjer-Nielsen L, Miles JJ, Wilce MC, Kostenko L, Borg NA, Williamson NA, Beddoe T, Purcell AW, Burrows SR, McCluskey J, Rossjohn J
Nat. Immunol. (2007) 8, 268-76 [doi:10.1038/ni1432]  [pubmed:17259989

Plasticity of the T cell receptor (TCR) is a hallmark of major histocompatibility complex (MHC)-restricted T cell recognition. However, it is unclear whether interactions of TCR and peptide-MHC class I (pMHCI) always conform to this paradigm. Here we describe the structure of a TCR, ELS4, in its non-ligand-bound form and in complex with a prominent 'bulged' Epstein-Barr virus peptide bound to HLA-B(*)3501. This complex was atypical of previously characterized TCR-pMHCI interactions in that a rigid face of the TCR crumpled the bulged antigenic determinant. This peptide 'bulldozing' created a more featureless pMHCI determinant, allowing the TCR to maximize MHC class I contacts essential for MHC class I restriction of TCR recognition. Our findings represent a mechanism of antigen recognition whereby the plasticity of the T cell response is dictated mainly by adjustments in the MHC-bound peptide.

Structure deposition and release

Deposited: 2006-11-16
Released: 2007-02-27
Revised: 2011-07-13

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication


Peptide details

Length: Undecamer (11 amino acids)

Sequence: EPLPQGQLTAY

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 GLU

TYR159
TYR7
ASN63
MET5
ARG62
TYR171
TRP167
TYR59
PHE33
P10 ALA

ASN80
THR73
LYS146
TRP147
GLU76
SER77
THR143
P11 TYR

ILE124
TYR74
GLN96
TYR84
LEU81
ILE142
SER77
THR143
ASN80
SER116
LYS146
TRP147
ARG97
TYR123
ILE95
P2 PRO

TYR99
TYR159
ASN63
TYR7
PHE67
TYR9
ILE66
P3 LEU

ARG97
TYR99
TYR9
GLN155
ILE66
LEU156
TYR159
ASN70
P4 PRO

GLN155
ILE66
LEU163
TYR159
P5 GLN

TYR9
GLN155
ASN70
TYR74
ARG97
P6 GLY

THR69
THR73
ASN70
P7 GLN

THR73
P8 LEU

LYS146
VAL152
TRP147
ALA150
P9 THR

SER77
THR73
VAL152
TRP147
ARG97

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
LEU163
TRP167
TYR171
MET5
TYR59
ASN63
ILE66
TYR7
B Pocket

ALA24
VAL34
THR45
ASN63
ILE66
PHE67
TYR7
ASN70
TYR9
TYR99
C Pocket

ASN70
THR73
TYR74
TYR9
ARG97
D Pocket

ASP114
GLN155
LEU156
TYR159
LEU160
TYR99
E Pocket

ASP114
TRP147
VAL152
LEU156
ARG97
F Pocket

SER116
TYR123
THR143
LYS146
TRP147
SER77
ASN80
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. Beta 2 microglobulin
Beta 2 microglobulin
        10        20        30        40        50        60
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
        70        80        90
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

2. Class I alpha
HLA-B*35:01
IPD-IMGT/HLA
[ipd-imgt:HLA34423]
        10        20        30        40        50        60
GSHSMRYFYTAMSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRTEPRAPWIEQEGPEYW
        70        80        90       100       110       120
DRNTQIFKTNTQTYRESLRNLRGYYNQSEAGSHIIQRMYGCDLGPDGRLLRGHDQSAYDG
       130       140       150       160       170       180
KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRAYLEGLCVEWLRRYLENGKETLQ
       190       200       210       220       230       240
RADPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
       250       260       270
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

3. Peptide
EPLPQGQLTAY

4. T cell receptor alpha
T cell receptor alpha
TRAV1
        10        20        30        40        50        60
QNIDQPTEMTATEGAIVQINCTYQTSGFNGLFWYQQHAGEAPTFLSYNVLDGLEEKGRFS
        70        80        90       100       110       120
SFLSRSKGYSYLLLKELQMKDSASYLCAVQASGGSYIPTFGRGTSLIVHPYIQNPDPAVY
       130       140       150       160       170       180
QLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSD

FACANAFN

5. T cell receptor beta
T cell receptor beta
TRBV10
        10        20        30        40        50        60
DAGITQSPRHKVTETGTPVTLRCHQTENHRYMYWYRQDPGHGLRLIHYSYGVKDTDKGEV
        70        80        90       100       110       120
SDGYSVSRSKTEDFLLTLESATSSQTSVYFCATGTGDSNQPQHFGDGTRLSILEDLNKVF
       130       140       150       160       170       180
PPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVCTDPQPLKEQP
       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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Complete structures

Aligned structures [cif]
  1. 2NX5 assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 2NX5 assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 2NX5 assembly 1  
Peptide only [cif]
  1. 2NX5 assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/2nx5

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