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7LGT

HLA-B*07:02 binding "SPKLHFYYL" at 1.97Å 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', 'D']
2. Class I alpha
HLA-B*07:02
['A', 'C']
3. Peptide
SPKLHFYYL
['E', 'F']

Species

Locus / Allele group

HLA-B / HLA-B*07

Publication

CD8+ T��cells specific for an immunodominant SARS-CoV-2 nucleocapsid epitope cross-react with selective seasonal coronaviruses.

Lineburg KE, Grant EJ, Swaminathan S, Chatzileontiadou DSM, Szeto C, Sloane H, Panikkar A, Raju J, Crooks P, Rehan S, Nguyen AT, Lekieffre L, Neller MA, Tong ZWM, Jayasinghe D, Chew KY, Lobos CA, Halim H, Burrows JM, Riboldi-Tunnicliffe A, Chen W, D'Orsogna L, Khanna R, Short KR, Smith C, Gras S
Immunity (2021) [doi:10.1016/j.immuni.2021.04.006]  [pubmed:33945786] 

Directly ex vivo, peptide-specific CD8+ T cells are present at relatively low frequency and are typically in a resting state. This protocol details the expansion of memory peptide-specific CD8+ T cells by in vitro stimulation, which can be subsequently characterized using a range of assays including tetramer staining and intracellular cytokine staining. For complete details on the use and execution of this protocol, please refer to Lineburg et al. (2021).

Structure deposition and release

Deposited: 2021-01-21
Released: 2021-04-21
Revised: 2021-08-11

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: SPKLHFYYL

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 SER

TRP167
TYR159
TYR7
ARG62
TYR171
MET5
TYR59
ASN63
 P2 PRO

TYR7
TYR9
ILE66
ASN63
TYR67
GLU45
TYR99
ARG62
TYR159
 P3 LYS

TYR159
ARG156
TYR9
ILE66
TYR99
GLN155
GLN70
 P4 LEU

ALA69
GLN155
ILE66
GLN70
 P5 HIS

TYR9
TYR99
ASP114
SER97
TYR116
GLN70
THR73
ARG156
 P6 PHE

GLN70
THR73
 P7 TYR

LYS146
THR73
ARG156
GLU152
TRP147
ALA150
 P8 TYR

LYS146
GLU76
ASN80
THR73
TRP147
SER77
GLN72
 P9 LEU

LEU81
TRP147
ILE124
TYR84
LYS146
TYR116
LEU95
THR143
TYR123
SER77
ASN80

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
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEPSS
3. Peptide
SPKLHFYYL

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. 7LGT assembly 1  
  2. 7LGT assembly 2  

Components

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

Derived data

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

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.