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


1KTL

HLA-E*01:03 binding "VTAPRTLLL" at 3.10Å 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
HLA-E*01:03
['A', 'C']
3. Peptide
VTAPRTLLL
['P', 'Q']

Species


Locus / Allele group


Publication

HLA-E allelic variants. Correlating differential expression, peptide affinities, crystal structures, and thermal stabilities.

Strong RK, Holmes MA, Li P, Braun L, Lee N, Geraghty DE
J. Biol. Chem. (2003) 278, 5082-90 [doi:10.1074/jbc.M208268200]  [pubmed:12411439

Previous studies of HLA-E allelic polymorphism have indicated that balancing selection may be acting to maintain two major alleles in most populations, indicating that a functional difference may exist between the alleles. The alleles differ at only one amino acid position, where an arginine at position 107 in HLA-E*0101 (E(R)) is replaced by a glycine in HLA-E*0103 (E(G)). To investigate possible functional differences, we have undertaken a study of the physical and biochemical properties of these two proteins. By comparing expression levels, we found that whereas steady-state protein levels were similar, the two alleles did in fact differ with respect to cell surface levels. To help explain this difference, we undertook studies of the relative differences in peptide affinity, complex stability, and three-dimensional structure between the alleles. The crystal structures for HLA-E(G) complexed with two distinct peptides were determined, and both were compared with the HLA-E(R) structure. No significant differences in the structure of HLA-E were induced as a result of binding different peptides or by the allelic substitution at position 107. However, there were clear differences in the relative affinity for peptide of each heavy chain, which correlated with and may be explained by differences between their thermal stabilities. These differences were completely consistent with the relative levels of the HLA-E alleles on the cell surface and may indeed correlate with functional differences. This in turn may help explain the apparent balancing selection acting on this locus.

Structure deposition and release

Deposited: 2002-01-16
Released: 2003-02-25
Revised: 2021-10-27

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: VTAPRTLLL

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
TYR171
LEU5
TYR159
ARG62
TYR59
THR163
TRP167
GLU63
P2 THR

GLU63
MET45
ALA67
TYR159
HIS9
SER66
TYR7
HIS99
SER24
P3 ALA

HIS99
GLN156
TRP97
TYR159
SER66
P4 PRO

TYR159
SER66
P5 ARG

GLN156
HIS155
TRP97
GLU152
P6 THR

TRP97
THR70
PHE74
PHE116
ILE73
GLU152
GLN156
P7 LEU

GLN156
PHE116
ILE73
TRP97
GLU152
ASN77
SER147
GLU114
TRP133
P8 LEU

LYS146
ILE73
VAL76
GLU152
ASN77
SER147
P9 LEU

LYS146
TYR123
LEU81
LEU95
PHE116
ASN77
LEU124
SER147
THR80
TYR84
ILE142
SER143

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
THR163
TRP167
TYR171
LEU5
TYR59
GLU63
SER66
TYR7
B Pocket

SER24
VAL34
MET45
GLU63
SER66
ALA67
TYR7
THR70
HIS9
HIS99
C Pocket

THR70
ILE73
PHE74
HIS9
TRP97
D Pocket

GLU114
HIS155
GLN156
TYR159
LEU160
HIS99
E Pocket

GLU114
SER147
GLU152
GLN156
TRP97
F Pocket

PHE116
TYR123
SER143
LYS146
SER147
ASN77
THR80
LEU81
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
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
        70        80        90
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

2. Class I alpha
HLA-E*01:03
IPD-IMGT/HLA
[ipd-imgt:HLA34202]
        10        20        30        40        50        60
GSHSLKYFHTSVSRPGRGEPRFISVGYVDDTQFVRFDNDAASPRMVPRAPWMEQEGSEYW
        70        80        90       100       110       120
DRETRSARDTAQIFRVNLRTLRGYYNQSEAGSHTLQWMHGCELGPDGRFLRGYEQFAYDG
       130       140       150       160       170       180
KDYLTLNEDLRSWTAVDTAAQISEQKSNDASEAEHQRAYLEDTCVEWLHKYLEKGKETLL
       190       200       210       220       230       240
HLEPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQQDGEGHTQDTELVETRPAGDGT
       250       260       270
FQKWAAVVVPSGEEQAYTCHVQHEGLPEPVTLRW

3. Peptide
VTAPRTLLL


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. 1KTL assembly 1  
  2. 1KTL assembly 2  

Components

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

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/1ktl

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