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5KD7

H2-Dd binding "IGPGRAFYV" at 2.35Å 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', 'G', 'J']
2. Class I alpha
H2-Dd
['A', 'C', 'F', 'I']
3. Peptide
IGPGRAFYV
['P', 'E', 'H', 'K']

Species


Locus / Allele group


Publication

Effects of Cross-Presentation, Antigen Processing, and Peptide Binding in HIV Evasion of T Cell Immunity.

Frey BF, Jiang J, Sui Y, Boyd LF, Yu B, Tatsuno G, Billeskov R, Solaymani-Mohammadi S, Berman PW, Margulies DH, Berzofsky JA
J. Immunol. (2018) [doi:10.4049/jimmunol.1701523]  [pubmed:29374075

Unlike cytosolic processing and presentation of viral Ags by virus-infected cells, Ags first expressed in infected nonprofessional APCs, such as CD4+ T cells in the case of HIV, are taken up by dendritic cells and cross-presented. This generally requires entry through the endocytic pathway, where endosomal proteases have first access for processing. Thus, understanding virus escape during cross-presentation requires an understanding of resistance to endosomal proteases, such as cathepsin S (CatS). We have modified HIV-1MN gp120 by mutating a key CatS cleavage site (Thr322Thr323) in the V3 loop of the immunodominant epitope IGPGRAFYTT to IGPGRAFYVV to prevent digestion. We found this mutation to facilitate cross-presentation and provide evidence from MHC binding and X-ray crystallographic structural studies that this results from preservation of the epitope rather than an increased epitope affinity for the MHC class I molecule. In contrast, when the protein is expressed by a vaccinia virus in the cytosol, the wild-type protein is immunogenic without this mutation. These proof-of-concept results show that a virus like HIV, infecting predominantly nonprofessional presenting cells, can escape T cell recognition by incorporating a CatS cleavage site that leads to destruction of an immunodominant epitope when the Ag undergoes endosomal cross-presentation.

Structure deposition and release

Deposited: 2016-06-07
Released: 2017-10-11
Revised: 2020-02-19

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: IGPGRAFYV

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 ILE

ARG66
LEU5
TRP167
ARG62
TYR159
TYR7
TYR171
TYR59
GLU163
GLU63
P2 GLY

TYR7
GLU63
ARG66
TYR159
P3 PRO

TRP97
TRP114
TYR159
TYR7
ASN70
ALA99
ARG66
P4 GLY

ASN70
ARG66
TRP97
TRP114
ASP156
P5 ARG

TRP147
PHE116
ASN70
ASP77
SER73
PHE74
TRP97
P6 ALA

ARG155
P7 PHE

ASP156
TRP147
ALA150
ALA152
ASP77
GLY151
ARG155
P8 TYR

TRP147
ASP77
SER73
VAL76
LYS146
THR143
P9 VAL

ASP77
TYR123
THR80
TRP147
ALA81
LYS146
TYR84
THR143

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

LEU159
CYS163
LEU167
LEU171
ARG5
TRP59
THR63
ALA66
PHE7
B Pocket

VAL24
ARG34
GLU45
THR63
ALA66
LYS67
PHE7
GLU70
THR9
GLY99
C Pocket

GLU70
PHE73
ARG74
THR9
MET97
D Pocket

GLN114
ASP155
ARG156
LEU159
GLU160
GLY99
E Pocket

GLN114
GLU147
ALA152
ARG156
MET97
F Pocket

ALA116
ILE123
ARG143
TRP146
GLU147
LEU77
ALA80
LEU81
TYR84
GLN95

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
WSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM

2. Class I alpha
H2-Dd
        10        20        30        40        50        60
SHSLRYFVTAVSRPGFGEPRYMEVGYVDNTEFVRFDSDAENPRYEPRARWIEQEGPEYWE
        70        80        90       100       110       120
RETRRAKGNEQSFRVDLRTALRYYNQSAGGSHTLQWMAGCDVESDGRLLRGYWQFAYDGC
       130       140       150       160       170       180
DYIALNEDLKTWTAADMAAQITRRKWEQAGAAERDRAYLEGECVEWLRRYLKNGNATLLR
       190       200       210       220       230       240
TDPPKAHVTHHRRPEGDVTLRCWALGFYPADITLTWQLNGEELTQEMELVETRPAGDGTF
       250       260       270
QKWASVVVPLGKEQKYTCHVEHEGLPEPLTLRWGK

3. Peptide
IGPGRAFYV


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. 5KD7 assembly 1  
  2. 5KD7 assembly 2  
  3. 5KD7 assembly 3  
  4. 5KD7 assembly 4  

Components

MHC Class I alpha chain [cif]
  1. 5KD7 assembly 1  
  2. 5KD7 assembly 2  
  3. 5KD7 assembly 3  
  4. 5KD7 assembly 4  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 5KD7 assembly 1  
  2. 5KD7 assembly 2  
  3. 5KD7 assembly 3  
  4. 5KD7 assembly 4  
Peptide only [cif]
  1. 5KD7 assembly 1  
  2. 5KD7 assembly 2  
  3. 5KD7 assembly 3  
  4. 5KD7 assembly 4  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/5kd7

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