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3NWM

Single chain construct of H2-Kd binding "None" 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

Single chain class i construct

1. Class I alpha
H2-Kd
['A']

Species


Locus / Allele group


Publication

Structural and functional characterization of a single-chain peptide-MHC molecule that modulates both naive and activated CD8+ T cells.

Samanta D, Mukherjee G, Ramagopal UA, Chaparro RJ, Nathenson SG, DiLorenzo TP, Almo SC
Proc. Natl. Acad. Sci. U.S.A. (2011) 108, 13682-7 [doi:10.1073/pnas.1110971108]  [pubmed:21825122

Peptide-MHC (pMHC) multimers, in addition to being tools for tracking and quantifying antigen-specific T cells, can mediate downstream signaling after T-cell receptor engagement. In the absence of costimulation, this can lead to anergy or apoptosis of cognate T cells, a property that could be exploited in the setting of autoimmune disease. Most studies with class I pMHC multimers used noncovalently linked peptides, which can allow unwanted CD8(+) T-cell activation as a result of peptide transfer to cellular MHC molecules. To circumvent this problem, and given the role of self-reactive CD8(+) T cells in the development of type 1 diabetes, we designed a single-chain pMHC complex (scK(d).IGRP) by using the class I MHC molecule H-2K(d) and a covalently linked peptide derived from islet-specific glucose-6-phosphatase catalytic subunit-related protein (IGRP(206-214)), a well established autoantigen in NOD mice. X-ray diffraction studies revealed that the peptide is presented in the groove of the MHC molecule in canonical fashion, and it was also demonstrated that scK(d).IGRP tetramers bound specifically to cognate CD8(+) T cells. Tetramer binding induced death of naive T cells and in vitro- and in vivo-differentiated cytotoxic T lymphocytes, and tetramer-treated cytotoxic T lymphocytes showed a diminished IFN-γ response to antigen stimulation. Tetramer accessibility to disease-relevant T cells in vivo was also demonstrated. Our study suggests the potential of single-chain pMHC tetramers as possible therapeutic agents in autoimmune disease. Their ability to affect the fate of naive and activated CD8(+) T cells makes them a potential intervention strategy in early and late stages of disease.

Structure deposition and release

Deposited: 2010-07-09
Released: 2011-07-06
Revised: 2017-06-28

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

ARG159
GLY163
PHE167
GLY171
LYS5
PRO59
ILE63
LEU66
ASN7
B Pocket

GLY24
GLN34
LYS45
ILE63
LEU66
LYS67
ASN7
LYS70
PHE9
THR99
C Pocket

LYS70
PRO73
LYS74
PHE9
THR97
D Pocket

ALA114
THR155
ALA156
ARG159
PRO160
THR99
E Pocket

ALA114
PRO147
TYR152
ALA156
THR97
F Pocket

PRO116
ARG123
GLY143
GLY146
PRO147
MET77
MET80
SER81
LYS84
GLU95

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-Kd
        10        20        30        40        50        60
MVYLKTNVFLGGGASGGGGSGGGGSMIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPH
        70        80        90       100       110       120
IEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHASMAEPKTVY
       130       140       150       160       170       180
WDRDMGGGGSGGGGSGGGGSGGGGSGPHSLRYFVTAVSRPGLGEPRFIAVGYVDDTQFVR
       190       200       210       220       230       240
FDSDADNPRFEPRAPWMEQEGPEYWEEQTQRAKSDEQWFRVSLRTAQRYYNQSKGGSHTF
       250       260       270       280       290       300
QRMFGCDVGSDWRLLRGYQQFAYDGRDYIALNEDLKTWTAADTAALITRRKWEQAGDAEY
       310       320       330       340       350       360
YRAYLEGECVEWLRRYLELGNETLLRTDSPKAHVTYHPRSQVDVTLRCWALGFYPADITL
       370       380       390       400       410       420
TWQLNGEDLTQDMELVETRPAGDGTFQKWAAVVVPLGKEQNYTCHVHHKGLPEPLTLRWA
       430       440
AAGGTGGLNDIFEAQKIEWHEGL


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. 3NWM assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 3NWM assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 3NWM assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/3nwm

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