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5F1I

DLA-88*50801: binding "KLFSGELTK" at 2.90Å 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', 'E', 'H', 'K', 'N', 'Q', 'T', 'W']
2. Class I alpha
DLA-88*50801:
['A', 'D', 'G', 'J', 'M', 'P', 'S', 'V']
3. Peptide
KLFSGELTK
['C', 'F', 'I', 'L', 'O', 'R', 'U', 'X']

Species

Locus / Allele group

DLA-88 / DLA-88*50801

Publication

Diversified Anchoring Features the Peptide Presentation of DLA-88*50801: First Structural Insight into Domestic Dog MHC Class I.

Xiao J, Xiang W, Chai Y, Haywood J, Qi J, Ba L, Qi P, Wang M, Liu J, Gao GF
J. Immunol. (2016) 197, 2306-15 [doi:10.4049/jimmunol.1600887]  [pubmed:27511732] 

Canines represent a crucial animal model for studying human diseases and organ transplantation, as well as the evolution of domestic animals. MHCs, with a central role in cellular immunity, are commonly used in the study of dog population genetics and genome evolution. However, the molecular basis for the peptide presentation of dog MHC remains largely unknown. In this study, peptide presentation by canine MHC class I DLA-88*50801 was structurally determined, revealing diversified anchoring modes of the binding peptides. Flexible and large pockets composed of both hydrophobic and hydrophilic residues can accommodate pathogen-derived peptides with diverse anchor residues, as confirmed by thermostability measurements. Furthermore, DLA-88*50801 contains an unusual α2 helix with a large coil in the TCR contact region. These results further our understanding of canine T cell immunity through peptide presentation of MHC class I and shed light on the molecular basis for vaccine development for canine infectious diseases, for example, canine distemper virus.

Structure deposition and release

Deposited: 2015-11-30
Released: 2016-11-30
Revised: 2016-11-30

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: KLFSGELTK

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 LYS

TRP168
TYR172
LEU5
TYR99
TYR59
GLU63
TYR7
LYS66
TYR160
THR164
 P2 LEU

VAL67
TYR99
ALA24
GLU63
LYS66
THR45
TYR160
TYR7
TYR9
 P3 PHE

TRP157
LYS66
THR70
TYR99
TYR160
GLN156
TYR9
 P4 SER

GLN156
LYS66
THR70
 P5 GLY

GLN156
 P6 GLU

TYR74
VAL73
ARG114
TRP147
GLN156
TRP157
VAL152
 P7 LEU

ALA150
VAL152
LYS146
TRP147
GLN156
 P8 THR

LYS146
VAL76
VAL73
TRP147
ASP77
 P9 LYS

ASP116
LYS146
ILE95
THR143
TYR74
THR97
THR80
ARG114
TRP147
TYR84
TYR123
ASP77
LEU81

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]

Chain sequences

1. Beta 2 microglobulin
Beta 2 microglobulin
        10        20        30        40        50        60
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
        70        80        90
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM
2. Class I alpha
DLA-88*50801:
        10        20        30        40        50        60
GSHSLRYFYTSVSRPGRGDPRFIAVGYVDDTQFVRFDSDAATGRTEPRAPWVEQEGPEYW
        70        80        90       100       110       120
DGETRKVKETAQVYRVDLDTLRGYYNQSEAGSHTIQTMYGCDLGPGGRLLRGYRQDAYDG
       130       140       150       160       170       180
ADYIALNEDLRSWTAADTAAQITRRKWEAAGVAELQWRNYLETTCVEWLQRYLEMGKETL
       190       200       210       220       230       240
LRAEPPSTRVTRHPISDHEVTLRCWALGFYPAEITLTWQRDGEDQTQDTEVVDTRPAGDG
       250       260       270
TFQKWAAVVVPSGQEQRYTCHVQHEGLVEPVTRRW
3. Peptide
KLFSGELTK

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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   e.g. load http://www.histo.fyi/structures/downloads/1hhk_1_peptide.cif
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. 5F1I assembly 1  
  2. 5F1I assembly 2  
  3. 5F1I assembly 3  
  4. 5F1I assembly 4  
  5. 5F1I assembly 5  
  6. 5F1I assembly 6  
  7. 5F1I assembly 7  
  8. 5F1I assembly 8  

Components

MHC Class I alpha chain [cif]
  1. 5F1I assembly 1  
  2. 5F1I assembly 2  
  3. 5F1I assembly 3  
  4. 5F1I assembly 4  
  5. 5F1I assembly 5  
  6. 5F1I assembly 6  
  7. 5F1I assembly 7  
  8. 5F1I assembly 8  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 5F1I assembly 1  
  2. 5F1I assembly 2  
  3. 5F1I assembly 3  
  4. 5F1I assembly 4  
  5. 5F1I assembly 5  
  6. 5F1I assembly 6  
  7. 5F1I assembly 7  
  8. 5F1I assembly 8  
Peptide only [cif]
  1. 5F1I assembly 1  
  2. 5F1I assembly 2  
  3. 5F1I assembly 3  
  4. 5F1I assembly 4  
  5. 5F1I assembly 5  
  6. 5F1I assembly 6  
  7. 5F1I assembly 7  
  8. 5F1I assembly 8  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/5f1i

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


Creative Commons Licence
This work is licensed under a Creative Commons Attribution 4.0 International License.