Alpha This is a work in progress and may change. Your feedback is very welcome.
  


4D0D

Gaga-BF2*002:01 binding "VIFPAKSL" at 3.13Å 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', 'E', 'H', 'K']
2. Class I alpha
Gaga-BF2*002:01
['A', 'D', 'G', 'J']
3. Peptide
VIFPAKSL
['C', 'F', 'I', 'L']

Species


Locus / Allele group


Publication

Expression levels of MHC class I molecules are inversely correlated with promiscuity of peptide binding.

Chappell P, Meziane EK, Harrison M, Magiera ��, Hermann C, Mears L, Wrobel AG, Durant C, Nielsen LL, Buus S, Ternette N, Mwangi W, Butter C, Nair V, Ahyee T, Duggleby R, Madrigal A, Roversi P, Lea SM, Kaufman J
Elife (2015) 4, [doi:10.7554/elife.05345]  [pubmed:25860507

Highly polymorphic major histocompatibility complex (MHC) molecules are at the heart of adaptive immune responses, playing crucial roles in many kinds of disease and in vaccination. We report that breadth of peptide presentation and level of cell surface expression of class I molecules are inversely correlated in both chickens and humans. This relationship correlates with protective responses against infectious pathogens including Marek's disease virus leading to lethal tumours in chickens and human immunodeficiency virus infection progressing to AIDS in humans. We propose that differences in peptide binding repertoire define two groups of MHC class I molecules strategically evolved as generalists and specialists for different modes of pathogen resistance. We suggest that differences in cell surface expression level ensure the development of optimal peripheral T cell responses. The inverse relationship of peptide repertoire and expression is evidently a fundamental property of MHC molecules, with ramifications extending beyond immunology and medicine to evolutionary biology and conservation.

Structure deposition and release

Deposited: 2014-04-25
Released: 2015-05-06
Revised: 2019-03-27

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: VIFPAKSL

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

TYR7
TYR58
THR160
TRP164
TYR168
TYR156
GLN62
P2 ILE

GLY66
ILE65
TYR156
TYR7
GLN62
ASN69
TYR43
ASP24
TYR97
P3 PHE

ARG9
ASN69
TYR97
TYR149
ILE65
TYR156
GLY152
LEU153
TYR111
P4 PRO

ASN69
TYR149
ILE65
P5 ALA

ILE72
TYR149
ASN69
ASP73
ARG9
P6 LYS

LYS143
TRP144
GLY147
ASN76
ILE72
TYR149
P7 SER

TRP144
ASN76
ILE79
ILE72
LYS143
P8 LEU

ASN76
PRO139
ARG83
MET113
THR140
ILE79
PHE120
LYS143
LEU80
TRP144

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]


Chain sequences

1. Beta 2 microglobulin
Beta 2 microglobulin
        10        20        30        40        50        60
DLTPKVQVYSRFPASAGTKNVLNCFAAGFHPPKISITLMKDGVPMEGAQYSDMSFNDDWT
        70        80        90
FQRLVHADFTPSSGSTYACKVEHETLKEPQVYKWDPEF

2. Class I alpha
Gaga-BF2*002:01
        10        20        30        40        50        60
ELHTLRYIRTAMTDPGPGLPWYVDVGYVDGELFVHYNSTARRYVPRTEWIAAKADQQYWD
        70        80        90       100       110       120
GQTQIGQGNEQIDRENLGILQRRYNQTGGSHTVQWMYGCDILEGGPIRGYYQMAYDGRDF
       130       140       150       160       170       180
TAFDKGTMTFTAAVPEAVPTKRKWEEGDYAEGLKQYLEETCVEWLRRYVEYGKAELGRRE
       190       200       210       220       230       240
RPEVRVWGKEADGILTLSCRAHGFYPRPIVVSWLKDGAVRGQDAHSGGIVPNGDGTYHTW
       250       260       270       280       290       300
VTIDAQPGDGDKYQCRVEHASLPQPGLYSWEPRSGGGLNDIFEAQKIEWHENSSSVDKLA

AALEHHHHHH

3. Peptide
VIFPAKSL


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.
Clicking on the clipboard icon will copy the url for the data to your clipboard.
This can then be used to load the structure/data directly from the url into an application like PyMol (for 3D structures) using the load command:
   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. 4D0D assembly 1  
  2. 4D0D assembly 2  
  3. 4D0D assembly 3  
  4. 4D0D assembly 4  

Components

MHC Class I alpha chain [cif]
  1. 4D0D assembly 1  
  2. 4D0D assembly 2  
  3. 4D0D assembly 3  
  4. 4D0D assembly 4  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 4D0D assembly 1  
  2. 4D0D assembly 2  
  3. 4D0D assembly 3  
  4. 4D0D assembly 4  
Peptide only [cif]
  1. 4D0D assembly 1  
  2. 4D0D assembly 2  
  3. 4D0D assembly 3  
  4. 4D0D assembly 4  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/4d0d

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