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2YEZ

Gaga-BF2*021:01 binding "TNPESKVFYL" at 2.90Å 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
Gaga-BF2*021:01
['A']
3. Peptide
TNPESKVFYL
['C']

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: 2011-03-31
Released: 2012-04-11
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: Decamer (10 amino acids)

Sequence: TNPESKVFYL

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 THR

TYR156
TYR7
TYR168
GLU62
LEU5
TYR58
THR160
TRP164
P10 LEU

ASN73
VAL121
PHE120
PRO139
LYS143
TRP95
ILE79
ASN76
LEU80
VAL93
ALA113
THR140
ARG83
P2 ASN

ASP24
TYR156
MET34
GLU62
TYR7
ILE65
VAL66
ARG9
P3 PRO

TYR7
ILE65
SER97
ARG9
TYR156
HIS111
P4 GLU

ILE65
TYR156
GLY152
LEU153
P5 SER

GLY68
ILE65
ILE72
SER69
P6 LYS

ILE72
TYR149
TRP144
P7 VAL

HIS111
TRP95
TYR149
TRP144
GLY152
LEU153
P8 PHE

ILE72
SER69
ASN73
HIS111
TRP144
TRP95
ASN76
SER97
ARG9
P9 TYR

ILE72
ASN76
TYR149
GLU75
TRP144
TRP95
THR140

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*021:01
        10        20        30        40        50        60
MGSCGALGLGLLLAAVCGAAAELHTLRYIRTAMTDPGPGLPWFVDVGYVDGELFMHYNST
        70        80        90       100       110       120
ARRAVPRTEWIAANTDQQYWDRETQIVQGSEQINRENLDILRRRYNQTGGSHTVQWMSGC
       130       140       150       160       170       180
DILEDGTIRGYHQAAYDGRDFVAFDKGTMTLTAAVPEAVPTKRKWEEGGYAEGLKQYLEE
       190       200       210       220       230       240
TCVEWLRRYVEYGKAELGRRERPEVRVWGKEADGILTLSCRAHGFYPRPIVVSWLKDGAV
       250       260       270       280       290       300
RGQDAQSGGIVPNGDGTYHTWVTIDAQPGDGDKYQCRVEHASLPQPGLYSWRSGGGLNDI
       310       320
FEAQKIEWHENSSSVDKLAAALEHHHHHH

3. Peptide
TNPESKVFYL


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. 2YEZ assembly 1  

Components

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

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/2yez

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