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6GH4

HLA-E*01:03 binding "RQPAKAPLL" at 2.16Å 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', 'F', 'H']
2. Class I alpha
HLA-E*01:03
['A', 'C', 'E', 'G']
3. Peptide
RQPAKAPLL
['P', 'Q', 'R', 'Y']

Species


Locus / Allele group


Publication

Pathogen-derived HLA-E bound epitopes reveal broad primary anchor pocket tolerability and conformationally malleable peptide binding.

Walters LC, Harlos K, Brackenridge S, Rozbesky D, Barrett JR, Jain V, Walter TS, O'Callaghan CA, Borrow P, Toebes M, Hansen SG, Sacha JB, Abdulhaqq S, Greene JM, Früh K, Marshall E, Picker LJ, Jones EY, McMichael AJ, Gillespie GM
Nat Commun (2018) 9, 3137 [doi:10.1038/s41467-018-05459-z]  [pubmed:30087334

The original version of this Article contained an error in the spelling of the author Jonah B Sacha, which was incorrectly given as Jonah Sacha. These errors have now been corrected in both the PDF and HTML versions of the Article.

Structure deposition and release

Deposited: 2018-05-04
Released: 2018-08-08
Revised: 2018-08-22

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: RQPAKAPLL

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 ARG

TRP167
LEU5
TYR171
TYR7
TYR159
THR163
TYR59
GLU63
ARG62
P2 GLN

HIS9
MET45
HIS99
SER24
GLU63
SER66
ALA67
TYR159
TYR7
THR70
P3 PRO

THR70
TRP97
TYR159
HIS99
GLN156
SER66
P4 ALA

ASP69
SER66
THR70
P5 LYS

GLU152
GLN156
TRP97
P6 ALA

ILE73
TRP97
THR70
PHE74
P7 PRO

GLU152
ASN77
PHE116
GLU114
GLN156
ILE73
TRP97
TRP133
P8 LEU

VAL76
SER143
ILE73
SER147
LYS146
ASN77
P9 LEU

PHE116
LYS146
TYR84
ASN77
TYR123
LEU95
THR80
LEU124
SER143
LEU81
ILE142

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
FQKWAAVVVPSGEEQRYTCHVQHEGLPEPVTLRW

3. Peptide
RQPAKAPLL


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.
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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. 6GH4 assembly 1  
  2. 6GH4 assembly 2  
  3. 6GH4 assembly 3  
  4. 6GH4 assembly 4  

Components

MHC Class I alpha chain [cif]
  1. 6GH4 assembly 1  
  2. 6GH4 assembly 2  
  3. 6GH4 assembly 3  
  4. 6GH4 assembly 4  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 6GH4 assembly 1  
  2. 6GH4 assembly 2  
  3. 6GH4 assembly 3  
  4. 6GH4 assembly 4  
Peptide only [cif]
  1. 6GH4 assembly 1  
  2. 6GH4 assembly 2  
  3. 6GH4 assembly 3  
  4. 6GH4 assembly 4  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/6gh4

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