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7CJQ

DLA-88*001:01: binding "RTISYTYPF" 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

1. Beta 2 microglobulin
['B', 'E']
2. Class I alpha
DLA-88*001:01:
['A', 'D']
3. Peptide
RTISYTYPF
['C', 'F']

Species

Locus / Allele group

DLA-88 / DLA-88*001

Publication

Structure of canine MHC class I at 2.7 Angstroms resolution

Sun, Y.J., Ma, L.Z., Li, S.

Structure deposition and release

Deposited: 2020-07-12
Released: 2020-08-26
Revised: 2020-09-30

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: RTISYTYPF

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 ARG

TYR160
TYR60
ARG63
TYR8
LEU6
THR164
GLU64
TRP168
TYR172
 P2 THR

THR67
TYR8
TYR100
MET46
GLU64
VAL68
TYR160
TYR10
 P3 ILE

HIS156
ARG74
ASP157
THR67
THR71
TYR100
TYR160
TYR10
 P4 SER

THR67
THR71
GLU70
ARG74
ARG63
 P5 TYR

HIS156
ARG74
 P6 THR

TYR10
TYR75
THR71
ARG74
 P7 TYR

HIS156
ASP157
ASP78
THR153
TRP148
GLY152
ALA151
 P8 PRO

ASP78
LYS147
TRP148
THR144
 P9 PHE

ARG96
ILE125
THR81
TYR124
ASP78
TYR85
ASP117
THR144
LYS147
LEU82
TRP148

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
MVQHPPKIQVYSRHPAENGKPNFLNCYVSGFHPPEIEIDLLKNGKEMKAEQTDLSFSKDW
        70        80        90
TFYLLVHTEFTPNEQDEFSCRVKHVTLSEPQIVKWDRDN
2. Class I alpha
DLA-88*001:01:
        10        20        30        40        50        60
GSHSLRYFYTSVSRPGRGDPRFIAVGYVDDTQFVRFDSDAATGRMEPRAPWMEQEGPEYW
        70        80        90       100       110       120
DRETRTVKETAQRYRVDLDTLRGYYNQSEAGSHTRQTMYGCDLGPGGRLLRGYSQDAYDG
       130       140       150       160       170       180
ADYIALNEDLRSWTAADTAAQITRRKWEAAGTAEHDRNYLETTCVEWLRRYLEMGKETLL
       190       200       210       220       230       240
RAEPPSTRVTRHPISDHEVTLRCWALGFYPAEITLTWQRDGEDQTQDTEVVDTRPAGDGT
       250       260       270
FQKWAAVVVPSGQEQRYTCHVQHEGLAEPVTRRWE
3. Peptide
RTISYTYPF

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. 7CJQ assembly 1  
  2. 7CJQ assembly 2  

Components

MHC Class I alpha chain [cif]
  1. 7CJQ assembly 1  
  2. 7CJQ assembly 2  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 7CJQ assembly 1  
  2. 7CJQ assembly 2  
Peptide only [cif]
  1. 7CJQ assembly 1  
  2. 7CJQ assembly 2  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/7cjq

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.