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1MHE

HLA-E*01:01 binding "VMAPRTVLL" at 2.85Å 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*01:01
['A', 'C']
3. Peptide
VMAPRTVLL
['P', 'Q']

Species


Locus / Allele group


Publication

Structural features impose tight peptide binding specificity in the nonclassical MHC molecule HLA-E.

O'Callaghan CA, Tormo J, Willcox BE, Braud VM, Jakobsen BK, Stuart DI, McMichael AJ, Bell JI, Jones EY
Mol. Cell (1998) 1, 531-41 [doi:10.1016/s1097-2765(00)80053-2]  [pubmed:9660937

The crystal structure of the nonclassical human class lb MHC molecule HLA-E has been determined in complex with a prototypic ligand, the nonamer peptide (VMAPRTVLL), derived from the highly conserved residues 3-11 of the human MHC class la leader sequence. The mode of peptide binding retains some of the standard features observed in MHC class la complexes, but novel features imply that HLA-E has evolved to mediate specific binding to a tightly defined set of almost identical hydrophobic peptides from the highly conserved class l leader sequences. These molecular adaptations make HLA-E a rigorous checkpoint at the cell surface reporting on the integrity of the antigen processing pathway to CD94/NKG2 receptor-bearing natural killer cells.

Structure deposition and release

Deposited: 1998-08-24
Released: 1999-03-23
Revised: 2011-07-13

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: VMAPRTVLL

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
ARG62
LEU5
TYR159
TRP167
TYR59
TYR171
GLU63
THR163
P2 MET

ALA67
THR70
HIS99
SER24
GLU63
MET45
TYR159
TYR59
TYR7
HIS9
SER66
P3 ALA

TYR7
GLN156
TYR159
HIS9
THR70
HIS99
SER66
TRP97
P4 PRO

SER66
TYR159
P5 ARG

GLN156
TRP97
ALA150
HIS155
GLU152
P6 THR

PHE116
ILE73
GLU152
ASN77
GLN156
TRP97
THR70
PHE74
P7 VAL

PHE74
PHE116
GLU114
ASN77
ILE73
TRP133
GLU152
GLN156
SER147
TRP97
P8 LEU

LYS146
THR80
VAL76
ASN77
ILE73
GLU152
SER147
P9 LEU

SER147
THR80
TYR84
LEU81
LEU95
ASN77
LYS146
ILE73
SER143
TYR123
PHE116
LEU124

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*01:01
IPD-IMGT/HLA
[ipd-imgt:HLA34073]
        10        20        30        40        50        60
GSHSLKYFHTSVSRPGRGEPRFISVGYVDDTQFVRFDNDAASPRMVPRAPWMEQEGSEYW
        70        80        90       100       110       120
DRETRSARDTAQIFRVNLRTLRGYYNQSEAGSHTLQWMHGCELGPDRRFLRGYEQFAYDG
       130       140       150       160       170       180
KDYLTLNEDLRSWTAVDTAAQISEQKSNDASEAEHQRAYLEDTCVEWLHKYLEKGKETLL
       190       200       210       220       230       240
HLEPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQQDGEGHTQDTELVETRPAGDGT
       250       260       270
FQKWAAVVVPSGEEQRYTCHVQHEGLPEPVTLRW

3. Peptide
VMAPRTVLL


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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   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. 1MHE assembly 1  

Components

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

Derived data

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

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