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6VQ2

HLA-B*27:05 binding "KRWIILGLNKIVRM" at 2.25Å 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*27:05
['A']
3. Peptide
KRWIILGLNKIVRM
['C']

Species


Locus / Allele group


Publication

Epitope length variants balance protective immune responses and viral escape in HIV-1 infection

Pymm, P., Tenzer, S., Wee, E., Weimershaus, M., Burgevin, A., Kollnberger, S., Gerstoft, J., Josephs, T.M., Ladell, K., McLaren, J.E., Appay, V., Price, D.A., Fugger, L., Bell, J.I., Schild, H., van Endert, P., Harkiolaki, M., Iversen, A.K.
(2022) 38, - [doi:10.1016/j.celrep.2022.110449

Cytotoxic T lymphocyte (CTL) and natural killer (NK) cell responses to a single optimal 10-mer epitope (KK10) in the human immunodeficiency virus type-1 (HIV-1) protein p24Gag are associated with enhanced immune control in patients expressing human leukocyte antigen (HLA)-B27:05. We find that proteasomal activity generates multiple length variants of KK10 (4-14 amino acids), which bind TAP and HLA-B27:05. However, only epitope forms ≥8 amino acids evoke peptide length-specific and cross-reactive CTL responses. Structural analyses reveal that all epitope forms bind HLA-B27:05 via a conserved N-terminal motif, and competition experiments show that the truncated epitope forms outcompete immunogenic epitope forms for binding to HLA-B27:05. Common viral escape mutations abolish (L136M) or impair (R132K) production of KK10 and longer epitope forms. Peptide length influences how well the inhibitory NK cell receptor KIR3DL1 binds HLA-B27:05 peptide complexes and how intraepitope mutations affect this interaction. These results identify a viral escape mechanism from CTL and NK responses based on differential antigen processing and peptide competition.

Structure deposition and release

Deposited: 2020-02-04
Released: 2021-02-10
Revised: 2022-03-09

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication


Peptide details

Length: Tetradecamer (14 amino acids)

Sequence: KRWIILGLNKIVRM

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 LYS

PHE33
MET5
TYR171
TYR59
TYR7
GLU63
TYR159
GLU163
TRP167
P11 ILE

THR73
P12 VAL

VAL152
ASP77
THR73
TRP147
P13 ARG

TRP147
THR143
GLU76
LYS146
ASP77
P14 MET

ILE124
ASP116
TYR84
TYR123
LYS146
ASP77
THR80
LEU95
TRP147
THR143
LEU81
ILE142
P2 ARG

GLY26
GLU45
TYR99
THR24
GLU63
CYS67
TYR159
GLU163
HIS9
VAL34
TYR7
VAL25
ILE66
P3 TRP

HIS114
TYR99
VAL152
LEU156
ILE66
GLN155
TYR159
P4 ILE

ALA69
ARG62
ILE66
P5 ILE

VAL152
GLN155
P6 LEU

ARG62
GLN155

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
GLU63
ILE66
TYR7
B Pocket

THR24
VAL34
GLU45
GLU63
ILE66
CYS67
TYR7
LYS70
HIS9
TYR99
C Pocket

LYS70
THR73
ASP74
HIS9
ASN97
D Pocket

HIS114
GLN155
LEU156
TYR159
LEU160
TYR99
E Pocket

HIS114
TRP147
VAL152
LEU156
ASN97
F Pocket

ASP116
TYR123
THR143
LYS146
TRP147
ASP77
THR80
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*27:05
IPD-IMGT/HLA
[ipd-imgt:HLA34811]
        10        20        30        40        50        60
GSHSMRYFHTSVSRPGRGEPRFITVGYVDDTLFVRFDSDAASPREEPRAPWIEQEGPEYW
        70        80        90       100       110       120
DRETQICKAKAQTDREDLRTLLRYYNQSEAGSHTLQNMYGCDVGPDGRLLRGYHQDAYDG
       130       140       150       160       170       180
KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRAYLEGECVEWLRRYLENGKETLQ
       190       200       210       220       230       240
RADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
       250       260       270
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

3. Peptide
KRWIILGLNKIVRM


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. 6VQ2 assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 6VQ2 assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 6VQ2 assembly 1  
Peptide only [cif]
  1. 6VQ2 assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/6vq2

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