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2QRI

Single chain construct of H2-Kb binding "None" at 2.00Å 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

Single chain class i construct

1. Class I alpha
H2-Kb
['A', 'B']

Species


Locus / Allele group


Publication

Structural engineering of pMHC reagents for T cell vaccines and diagnostics.

Mitaksov V, Truscott SM, Lybarger L, Connolly JM, Hansen TH, Fremont DH
Chem. Biol. (2007) 14, 909-22 [doi:10.1016/j.chembiol.2007.07.010]  [pubmed:17719490

MHC class I peptide complexes (pMHC) are routinely used to enumerate T cell populations and are currently being evaluated as vaccines to tumors and specific pathogens. Herein, we describe the structures of three generations of single-chain pMHC progressively designed for the optimal presentation of covalently associated epitopes. Our ultimate design employs a versatile disulfide trap between an invariant MHC residue and a short C-terminal peptide extension. This general strategy is nondisruptive of native pMHC conformation and T cell receptor engagement. Indeed, cell-surface-expressed MHC complexes with disulfide-trapped epitopes are refractory to peptide exchange, suggesting they will make safe and effective vaccines. Furthermore, we find that disulfide-trap stabilized, recombinant pMHC reagents reliably detect polyclonal CD8 T cell populations as proficiently as conventional reagents and are thus well suited to monitor or modulate immune responses during pathogenesis.

Structure deposition and release

Deposited: 2007-07-28
Released: 2007-11-06
Revised: 2017-10-25

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication


Binding cleft pockets


Peptide sidechain binding pockets (static)
Peptide terminii and backbone binding residues (static)
A Pocket

LEU159
ARG163
VAL167
ASP171
PHE5
GLU59
LEU63
GLY66
LYS7
B Pocket

ILE24
SER34
ILE45
LEU63
GLY66
LYS67
LYS7
PRO70
GLY9
ASP99
C Pocket

PRO70
GLU73
MET74
GLY9
GLU97
D Pocket

LYS114
SER155
ARG156
LEU159
GLY160
ASP99
E Pocket

LYS114
LEU147
THR152
ARG156
GLU97
F Pocket

VAL116
GLY123
GLY143
SER146
LEU147
MET77
SER80
LYS81
SER84
PRO95

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. Class I alpha
H2-Kb
        10        20        30        40        50        60
SIINFEKLGGGASGGGGSGGGGSIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEI
        70        80        90       100       110       120
QMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDR
       130       140       150       160       170       180
DMGGGGSGGGGSGGGGSGGGGSGPHSLRYFVTAVSRPGLGEPRYMEVGYVDDTEFVRFDS
       190       200       210       220       230       240
DAENPRYEPRARWMEQEGPEYWERETQKAKGNEQSFRVDLRTLLGYYNQSKGGSHTIQVI
       250       260       270       280       290       300
SGCEVGSDGRLLRGYQQYAYDGCDYIALNEDLKTWTAADMAALITKHKWEQAGEAERLRA
       310       320       330       340       350       360
YLEGTCVEWLRRYLKNGNATLLRTDSPKAHVTHHSRPEDKVTLRCWALGFYPADITLTWQ
       370       380       390       400       410       420
LNGEELIQDMELVETRPAGDGTFQKWASVVVPLGKEQYYTCHVYHQGLPEPLTLRWEPPP

ST


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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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. 2QRI assembly 1  
  2. 2QRI assembly 2  

Components

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

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/2qri

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