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4CVX

Gaga-BF2*002:01 binding "YPYLGPNTL" at 3.30Å 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']
2. Class I alpha
Gaga-BF2*002:01
['A', 'D']
3. Peptide
YPYLGPNTL
['C', 'F']

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: 2014-03-31
Released: 2015-05-06
Revised: 2019-02-27

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: YPYLGPNTL

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 TYR

LEU5
ILE65
TYR58
TRP164
GLN62
TYR7
TYR168
GLY61
TYR156
P2 PRO

TYR7
ASP24
ASN69
TYR156
ILE65
TYR43
TYR97
GLN62
P3 TYR

TYR97
GLY152
ARG9
LEU153
TYR149
TYR156
ILE65
ASN69
TYR111
P4 LEU

ILE72
GLY68
GLN64
ILE65
ASN69
P5 GLY

ARG9
ILE72
ASN69
TYR111
P6 PRO

TYR111
TRP144
TYR149
P7 ASN

ILE72
TRP144
ASN76
TYR149
P8 THR

ILE79
ASN76
GLU75
ILE72
TRP144
P9 LEU

TRP144
ARG83
PHE120
ASN76
TRP95
ILE79
LEU80
MET113
PRO139
THR140
LYS143

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
YPYLGPNTL


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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   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. 4CVX assembly 1  
  2. 4CVX assembly 2  

Components

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

Derived data

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

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