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5KD4

H2-Dd binding "IGPGRAFYVI" at 3.05Å 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-Dd
['A', 'C']
3. Peptide
IGPGRAFYVI
['P', 'Q']

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: 2018-02-28

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication


Peptide details

Length: Decamer (10 amino acids)

Sequence: IGPGRAFYVI

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

GLU163
TRP167
ARG66
TYR159
ARG62
TYR7
TYR171
LEU5
TYR59
GLU63
P10 ILE

LYS146
ASP77
THR80
TYR84
ALA81
TYR123
TRP147
THR143
P2 GLY

GLU63
GLU163
ARG66
TYR159
TYR7
P3 PRO

TYR159
TYR7
TRP97
TRP114
ASN70
ALA99
ARG66
P4 GLY

ASN70
TRP97
TRP114
ARG66
ASP156
P5 ARG

PHE116
TRP147
TRP97
ASN70
PHE74
ASP77
SER73
P6 ALA

ASN70
P7 PHE

GLY69
GLN72
SER73
P8 TYR

ASP77
ARG155
GLY151
ALA150
TRP147
ALA152
P9 VAL

LYS146
ASP77
THR80
VAL76
SER73
TRP147

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
LEU5
TYR59
GLU63
ARG66
TYR7
B Pocket

GLU24
VAL34
TYR45
GLU63
ARG66
ALA67
TYR7
ASN70
VAL9
ALA99
C Pocket

ASN70
SER73
PHE74
VAL9
TRP97
D Pocket

TRP114
ARG155
ASP156
TYR159
LEU160
ALA99
E Pocket

TRP114
TRP147
ALA152
ASP156
TRP97
F Pocket

PHE116
TYR123
THR143
LYS146
TRP147
ASP77
THR80
ALA81
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
MIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKD
        70        80        90
WSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM

2. Class I alpha
H2-Dd
        10        20        30        40        50        60
MSHSLRYFVTAVSRPGFGEPRYMEVGYVDNTEFVRFDSDAENPRYEPRARWIEQEGPEYW
        70        80        90       100       110       120
ERETRRAKGNEQSFRVDLRTALRYYNQSAGGSHTLQWMAGCDVESDGRLLRGYWQFAYDG
       130       140       150       160       170       180
CDYIALNEDLKTWTAADMAAQITRRKWEQAGAAERDRAYLEGECVEWLRRYLKNGNATLL
       190       200       210       220       230       240
RTDPPKAHVTHHRRPEGDVTLRCWALGFYPADITLTWQLNGEELTQEMELVETRPAGDGT
       250       260       270
FQKWASVVVPLGKEQKYTCHVEHEGLPEPLTLRWGKE

3. Peptide
IGPGRAFYVI


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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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. 5KD4 assembly 1  
  2. 5KD4 assembly 2  

Components

MHC Class I alpha chain [cif]
  1. 5KD4 assembly 1  
  2. 5KD4 assembly 2  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 5KD4 assembly 1  
  2. 5KD4 assembly 2  
Peptide only [cif]
  1. 5KD4 assembly 1  
  2. 5KD4 assembly 2  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/5kd4

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