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3FON

H2-Kwm7 binding "VNDIFEAI" at 2.03Å 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
H2-Kwm7
['A', 'C']
3. Peptide
VNDIFEAI
['P', 'E']

Species


Locus / Allele group


Publication

Predominant occupation of the class I MHC molecule H-2Kwm7 with a single self-peptide suggests a mechanism for its diabetes-protective effect.

Brims DR, Qian J, Jarchum I, Mikesh L, Palmieri E, Ramagopal UA, Malashkevich VN, Chaparro RJ, Lund T, Hattori M, Shabanowitz J, Hunt DF, Nathenson SG, Almo SC, Dilorenzo TP
Int. Immunol. (2010) 22, 191-203 [doi:10.1093/intimm/dxp127]  [pubmed:20093428

Type 1 diabetes (T1D) is an autoimmune disease characterized by T cell-mediated destruction of insulin-producing pancreatic beta cells. In both humans and the non-obese diabetic (NOD) mouse model of T1D, class II MHC alleles are the primary determinant of disease susceptibility. However, class I MHC genes also influence risk. These findings are consistent with the requirement for both CD4(+) and CD8(+) T cells in the pathogenesis of T1D. Although a large body of work has permitted the identification of multiple mechanisms to explain the diabetes-protective effect of particular class II MHC alleles, studies examining the protective influence of class I alleles are lacking. Here, we explored this question by performing biochemical and structural analyses of the murine class I MHC molecule H-2K(wm7), which exerts a diabetes-protective effect in NOD mice. We have found that H-2K(wm7) molecules are predominantly occupied by the single self-peptide VNDIFERI, derived from the ubiquitous protein histone H2B. This unexpected finding suggests that the inability of H-2K(wm7) to support T1D development could be due, at least in part, to the failure of peptides from critical beta-cell antigens to adequately compete for binding and be presented to T cells. Predominant presentation of a single peptide would also be expected to influence T-cell selection, potentially leading to a reduced ability to select a diabetogenic CD8(+) T-cell repertoire. The report that one of the predominant peptides bound by T1D-protective HLA-A*31 is histone derived suggests the potential translation of our findings to human diabetes-protective class I MHC molecules.

Structure deposition and release

Deposited: 2008-12-30
Released: 2010-01-12
Revised: 2020-02-05

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication


Peptide details

Length: Octamer (8 amino acids)

Sequence: VNDIFEAI

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 VAL

TRP167
TYR159
ALA163
GLN63
LEU5
TYR59
TYR171
TYR7
P2 ASN

TYR45
TYR159
GLN63
TYR7
ASN70
VAL9
ILE66
ARG99
GLU24
P3 ASP

ILE66
ASN70
ARG99
TYR159
P4 ILE

ARG99
ASN70
ILE66
P5 PHE

GLN114
GLU24
ARG97
SER73
ASN70
ARG99
TYR22
VAL9
P6 GLU

ASP77
ALA150
ALA152
TRP147
GLY151
ARG155
ARG97
P7 ALA

ARG97
ASP77
LYS146
TRP147
SER73
P8 ILE

THR80
VAL116
ASP77
ILE95
ALA81
TYR123
TYR84
LYS146
TRP147
THR143
ARG97

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
ALA163
TRP167
TYR171
LEU5
TYR59
GLN63
ILE66
TYR7
B Pocket

GLU24
VAL34
TYR45
GLN63
ILE66
ALA67
TYR7
ASN70
VAL9
ARG99
C Pocket

ASN70
SER73
SER74
VAL9
ARG97
D Pocket

GLN114
ARG155
ASP156
TYR159
LEU160
ARG99
E Pocket

GLN114
TRP147
ALA152
ASP156
ARG97
F Pocket

VAL116
TYR123
THR143
LYS146
TRP147
ASP77
THR80
ALA81
TYR84
ILE95

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
MIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKD
        70        80        90
WSFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

2. Class I alpha
H2-Kwm7
        10        20        30        40        50        60
GSHSLRYFVTAVSRPGHGKPRYMEVGYVDDTEFVRFDSDAENPRYEPRTPWMEQVEPEYW
        70        80        90       100       110       120
EGQTQIAKGNEQSSRVDLRTALRYYNQSAGGSHTIQRMRGCEVGSDGRLLRGYQQVAYDG
       130       140       150       160       170       180
RDYIALNEDLKTWTAADMAALITKHKWEQAGAAERDRAYLEGACVEWLRRYLELGNATLL
       190       200       210       220       230       240
RTDSPKAHVTHHSRPKDKVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGT
       250       260       270
FQKWASVVVPLGKEQNYTCHVYHEGLPEPLTLRW

3. Peptide
VNDIFEAI


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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Complete structures

Aligned structures [cif]
  1. 3FON assembly 1  
  2. 3FON assembly 2  

Components

MHC Class I alpha chain [cif]
  1. 3FON assembly 1  
  2. 3FON assembly 2  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 3FON assembly 1  
  2. 3FON assembly 2  
Peptide only [cif]
  1. 3FON assembly 1  
  2. 3FON assembly 2  

Derived data

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

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