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3TID

H2-Kb binding "AVYNFATM" at 1.65Å 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

1. Beta 2 microglobulin
['B']
2. Class I alpha
H2-Kb
['A']
3. Peptide
AVYNFATM
['C']

Species


Locus / Allele group


Publication

Disparate epitopes mediating protective heterologous immunity to unrelated viruses share peptide-MHC structural features recognized by cross-reactive T cells.

Shen ZT, Nguyen TT, Daniels KA, Welsh RM, Stern LJ
J. Immunol. (2013) 191, 5139-52 [doi:10.4049/jimmunol.1300852]  [pubmed:24127554

Closely related peptide epitopes can be recognized by the same T cells and contribute to the immune response against pathogens encoding those epitopes, but sometimes cross-reactive epitopes share little homology. The degree of structural homology required for such disparate ligands to be recognized by cross-reactive TCRs remains unclear. In this study, we examined the mechanistic basis for cross-reactive T cell responses between epitopes from unrelated and pathogenic viruses, lymphocytic choriomeningitis virus (LCMV) and vaccinia virus. Our results show that the LCMV cross-reactive T cell response toward vaccinia virus is dominated by a shared asparagine residue, together with other shared structural elements conserved in the crystal structures of K(b)-VV-A11R and K(b)-LCMV-gp34. Based on analysis of the crystal structures and the specificity determinants for the cross-reactive T cell response, we were able to manipulate the degree of cross-reactivity of the T cell response, and to predict and generate a LCMV cross-reactive response toward a variant of a null OVA-derived peptide. These results indicate that protective heterologous immune responses can occur for disparate epitopes from unrelated viruses.

Structure deposition and release

Deposited: 2011-08-20
Released: 2012-08-22
Revised: 2016-05-11

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: AVYNFATM

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

P2 ALA

TRP167
GLU63
LEU5
TYR171
TYR159
LYS66
THR163
TYR59
TYR7
P3 VAL

GLU63
TYR45
ALA67
ASN70
GLU24
TYR159
TYR7
LYS66
P4 TYR

LEU156
ARG155
SER99
TYR159
GLN114
GLU152
ASN70
P5 ASN

ARG155
ASN70
LYS66
P6 PHE

ARG155
TYR22
SER73
SER99
GLU24
GLN114
ASN70
PHE74
VAL97
VAL9
TYR116
P7 ALA

ARG155
ASP77
TYR116
SER73
GLU152
TRP147
P8 THR

ASP77
SER73
TRP147
THR143
LYS146
P9 MET

TYR123
LYS146
TYR116
LEU81
ASP77
THR80
TYR84
TRP147
ILE95
ILE142
PHE74
THR143

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

GLU159
LEU163
LEU167
CYS171
PHE5
MET59
GLY63
TYR66
MET7
B Pocket

LEU24
TYR34
SER45
GLY63
TYR66
TRP67
MET7
GLU70
PRO9
SER99
C Pocket

GLU70
LYS73
ALA74
PRO9
GLY97
D Pocket

GLY114
GLU155
GLN156
GLU159
ALA160
SER99
E Pocket

GLY114
ALA147
HIS152
GLN156
GLY97
F Pocket

LEU116
TYR123
ALA143
ALA146
ALA147
ASN77
SER80
PHE81
ASP84
SER95

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
H2-Kb
        10        20        30        40        50        60
IQEEFKMGPHSLRYFVTAVSRPGLGEPRYMEVGYVDDTEFVRFDSDAENPRYEPRARWME
        70        80        90       100       110       120
QEGPEYWERETQKAKGNEQSFRVDLRTLLGYYNQSKGGSHTIQVISGCEVGSDGRLLRGY
       130       140       150       160       170       180
QQYAYDGRDYIALNEDLKTWTAADMAALITKHKWEQAGEAERLRAYLEGTCVEWLRRYLK
       190       200       210       220       230       240
NGNATLLRTDSPKAHVTHHSRPEDKVTLRCWALGFYPADITLTWQLNGEELIQDMELVET
       250       260       270       280
RPAGDGTFQKWASVVVPLGKEQYYTCHVYHQGLPEPLTLRWEPC

3. Peptide
AVYNFATM


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. 3TID assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 3TID assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 3TID assembly 1  
Peptide only [cif]
  1. 3TID assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/3tid

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