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7S8A

HLA-B*07:02 binding "EPRSPSHSM" at 2.10Å 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-B*07:02
['A']
3. Peptide
EPRSPSHSM
['C']

Species


Locus / Allele group


Publication

CRYSTAL STRUCTURE OF HLA-B*07:02 IN COMPLEX WITH PHOSPHOPEPTIDE NEOANTIGENS

Patskovska, L., Patskovsky, Y., Nyovanie, S., Nataragan, A., Joshi, B., Morin, B., Brittsan, C., Huber, O., Gordon, S., MIchelet, X., Schmitzberger, F., Stein, R., Findeis, M., Hurwitz, A., Van Dijk, M., Buell, J., Underwood, D., Krogsgaard, M.

Structure deposition and release

Deposited: 2021-09-17
Released: 2022-11-02
Revised: 2022-11-02

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: EPRSPSHSM

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 GLU

GLU163
TRP167
TYR171
PHE33
MET5
ARG62
TYR7
TYR159
TYR59
ASN63
P2 PRO

GLU45
TYR159
TYR9
ASN63
ILE66
TYR67
TYR99
TYR7
ARG62
P3 ARG

ARG62
TYR116
GLN155
GLN70
TYR159
ILE66
ASP114
TYR9
ARG156
TYR99
P5 PRO

THR73
ILE66
ALA69
GLN155
GLN70
P6 SER

ARG156
GLN155
THR73
GLU152
GLN70
P7 HIS

GLU152
ALA150
TRP147
LYS146
ARG156
SER77
THR73
P8 SER

LYS146
SER77
ASN80
THR73
GLU76
TRP147
P9 MET

ILE124
TRP147
TYR84
TYR123
LYS146
THR143
LEU81
ASN80
TYR116
LEU95
SER77

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
GLU163
TRP167
TYR171
MET5
TYR59
ASN63
ILE66
TYR7
B Pocket

SER24
VAL34
GLU45
ASN63
ILE66
TYR67
TYR7
GLN70
TYR9
TYR99
C Pocket

GLN70
THR73
ASP74
TYR9
SER97
D Pocket

ASP114
GLN155
ARG156
TYR159
LEU160
TYR99
E Pocket

ASP114
TRP147
GLU152
ARG156
SER97
F Pocket

TYR116
TYR123
THR143
LYS146
TRP147
SER77
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
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
        70        80        90
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

2. Class I alpha
HLA-B*07:02
IPD-IMGT/HLA
[ipd-imgt:HLA34746]
        10        20        30        40        50        60
GSHSMRYFYTSVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPREEPRAPWIEQEGPEYW
        70        80        90       100       110       120
DRNTQIYKAQAQTDRESLRNLRGYYNQSEAGSHTLQSMYGCDVGPDGRLLRGHDQYAYDG
       130       140       150       160       170       180
KDYIALNEDLRSWTAADTAAQITQRKWEAAREAEQRRAYLEGECVEWLRRYLENGKDKLE
       190       200       210       220       230       240
RADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
       250       260       270
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWE

3. Peptide
EPRSPSHSM


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. 7S8A assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 7S8A assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 7S8A assembly 1  
Peptide only [cif]
  1. 7S8A assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/7s8a

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