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6EI2

HLA-A*68:01 binding "ETSPLTAEKL" at 1.61Å 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
HLA-A*68:01
['A']
3. Peptide
ETSPLTAEKL
['C']

Species

Locus / Allele group

HLA-A / HLA-A*68

Publication

Crystal Structure of HLA-A68 presenting a C-terminally extended peptide

Picaud, S., Guillaume, P., Pike, A.C.W., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Gfeller, D., Filippakopoulos, P.

Structure deposition and release

Deposited: 2017-09-16
Released: 2017-10-11
Revised: 2017-10-11

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication

Peptide details

Length: Decamer (10 amino acids)

Sequence: ETSPLTAEKL

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 GLU

TYR31
TYR195
TRP191
MET29
PHE57
ARG86
TYR83
ASN87
ASN90
TYR183
THR187
 P11 THR

TYR31
MET69
VAL91
ARG86
ASN87
ASN90
TYR183
THR187
TYR123
TYR33
 P12 SER

ASN90
TYR183
TYR123
TRP180
TYR33
 P13 PRO

TYR183
ASN90
 P14 LEU

GLN94
GLN179
TYR183
VAL176
TRP180
 P15 THR

ASN90
ALA93
THR97
GLN94
 P16 ALA

VAL176
THR97
TRP171
ASP101
 P17 GLU

VAL100
THR97
TRP171
ASP101
LYS170
 P18 LYS

ASP140
THR167
LEU105
THR166
LYS170
ASP98
TYR147
ILE119
ARG138
ILE148
TRP171
ASP101
 P19 LEU

TYR147
TYR108
ALA163
THR104
ASP101
THR167
LEU105
THR166
LYS170

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

ALA159
GLY163
GLU167
ARG171
SER5
GLU59
ARG63
ARG66
ARG7
B Pocket

ILE24
PHE34
ARG45
ARG63
ARG66
ASN67
ARG7
ALA70
PHE9
MET99
C Pocket

ALA70
GLN73
THR74
PHE9
GLN97
D Pocket

TYR114
GLU155
GLN156
ALA159
TYR160
MET99
E Pocket

TYR114
LYS147
HIS152
GLN156
GLN97
F Pocket

GLN116
ASP123
THR143
HIS146
LYS147
VAL77
GLY80
THR81
GLY84
THR95

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
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
        70        80        90
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM
2. Class I alpha
HLA-A*68:01
IPD-IMGT/HLA
[ipd-imgt:HLA34091]
        10        20        30        40        50        60
MGSHSMRYFYTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
        70        80        90       100       110       120
WDRNTRNVKAQSQTDRVDLGTLRGYYNQSEAGSHTIQMMYGCDVGSDGRFLRGYRQDAYD
       130       140       150       160       170       180
GKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQWRAYLEGTCVEWLRRYLENGKETL
       190       200       210       220       230       240
QRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
       250       260       270
TFQKWVAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE
3. Peptide
ETSPLTAEKL

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. 6EI2 assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 6EI2 assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 6EI2 assembly 1  
Peptide only [cif]
  1. 6EI2 assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/6ei2

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.