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2XFX

BoLA-N*13:01 binding "VGYPKVKEEML" at 1.90Å 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

1. Beta 2 microglobulin
['B']
2. Class I alpha
BoLA-N*13:01
['A']
3. Peptide
VGYPKVKEEML
['C']

Species


Locus / Allele group


Publication

MHC class I bound to an immunodominant Theileria parva epitope demonstrates unconventional presentation to T cell receptors.

Macdonald IK, Harkiolaki M, Hunt L, Connelley T, Carroll AV, MacHugh ND, Graham SP, Jones EY, Morrison WI, Flower DR, Ellis SA
PLoS Pathog. (2010) 6, e1001149 [doi:10.1371/journal.ppat.1001149]  [pubmed:20976198

T cell receptor (TCR) recognition of peptide-MHC class I (pMHC) complexes is a crucial event in the adaptive immune response to pathogens. Peptide epitopes often display a strong dominance hierarchy, resulting in focusing of the response on a limited number of the most dominant epitopes. Such T cell responses may be additionally restricted by particular MHC alleles in preference to others. We have studied this poorly understood phenomenon using Theileria parva, a protozoan parasite that causes an often fatal lymphoproliferative disease in cattle. Despite its antigenic complexity, CD8+ T cell responses induced by infection with the parasite show profound immunodominance, as exemplified by the Tp1(214-224) epitope presented by the common and functionally important MHC class I allele N*01301. We present a high-resolution crystal structure of this pMHC complex, demonstrating that the peptide is presented in a distinctive raised conformation. Functional studies using CD8+ T cell clones show that this impacts significantly on TCR recognition. The unconventional structure is generated by a hydrophobic ridge within the MHC peptide binding groove, found in a set of cattle MHC alleles. Extremely rare in all other species, this feature is seen in a small group of mouse MHC class I molecules. The data generated in this analysis contribute to our understanding of the structural basis for T cell-dependent immune responses, providing insight into what determines a highly immunogenic p-MHC complex, and hence can be of value in prediction of antigenic epitopes and vaccine design.

Structure deposition and release

Deposited: 2010-05-28
Released: 2010-10-27
Revised: 2012-03-28

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: VGYPKVKEEML

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

P10 TYR

TYR99
ASN70
TYR159
ILE66
ALA152
PHE156
ARG155
P11 PRO

ARG155
ASN70
ARG62
ILE66
P12 LYS

HIS9
GLU114
ARG155
GLU97
GLU69
TRP73
TYR74
TYR116
ASN70
P13 VAL

ARG155
TRP73
P14 LYS

LEU72
GLU76
GLU69
TRP73
P15 GLU

ALA150
P16 GLU

MET147
GLY151
ARG155
ALA150
TRP73
ALA152
P17 MET

LYS146
SER143
GLU76
TRP73
ASN80
MET147
ALA77
P18 LEU

MET147
LEU95
TYR123
LYS146
TYR84
TRP73
TYR116
LEU81
SER143
LEU124
ILE142
ALA77
ASN80
P8 VAL

LEU5
TRP167
TYR159
TYR59
TYR7
ARG62
THR163
GLU63
TYR171
P9 GLY

TYR99
ARG62
TYR159
TYR7
ILE66
GLU63

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
ILE66
TYR7
B Pocket

THR24
VAL34
THR45
GLU63
ILE66
SER67
TYR7
ASN70
HIS9
TYR99
C Pocket

ASN70
TRP73
TYR74
HIS9
GLU97
D Pocket

GLU114
ARG155
PHE156
TYR159
LEU160
TYR99
E Pocket

GLU114
MET147
ALA152
PHE156
GLU97
F Pocket

TYR116
TYR123
SER143
LYS146
MET147
ALA77
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
AIQRPPKIQVYSRHPPEDGKPNYLNCYVYGFHPPQIEIDLLKNGEKIKSEQSDLSFSKDW
        70        80        90
SFYLLSHAEFTPNSKDQYSCRVKHVTLEQPRIVKWDRDL

2. Class I alpha
BoLA-N*13:01
        10        20        30        40        50        60
GSHSLRYFHTAVSRPGLREPLFITVGYVDDTQFVRFDSDARDPRTEPRQPWMEKEGPEYW
        70        80        90       100       110       120
DRETQISKENALWYREALNNLRGYYNQSEAGSHTLQEMYGCDVGSDGRLRRGYEQYGYDG
       130       140       150       160       170       180
RDYLALNEDLRSWTAADTAAQISKRKMEAAGAAERFRNYLEGTCVEWLRRYLENGKDTLL
       190       200       210       220       230       240
RADPPKAHVTRHPSSEHEVTLRCWALGFYPEEISLTWQRNGEDQTQDMELVETRPSGDGN
       250       260       270
FQKWAALVVPSGEEQRYTCRVQHEGLQEPLTLRWEPG

3. Peptide
VGYPKVKEEML


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. 2XFX assembly 1  

Components

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

Derived data

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

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