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.

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

Homo sapiens (Human)

Locus / Allele group

HLA-E / HLA-E*01

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-E01:01 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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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]

1MHE assembly 1

Components

MHC Class I alpha chain [cif]

1MHE assembly 1

MHC Class I antigen binding domain (alpha1/alpha2) [cif]

1MHE assembly 1

Peptide only [cif]

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

Protein Data Bank Europe - Coordinate Server
1HHK - HLA-A*02:01 binding LLFGYPVYV at 2.5Å resolution - PDB entry for 1HHK
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. - PyMol CEALIGN Method - Publication
PyMol - PyMol.org/pymol
Levenshtein distance - Wikipedia entry
Protein Data Bank Europe REST API - Molecules endpoint
3Dmol.js: molecular visualization with WebGL - 3DMol.js - Publication
Protein Data Bank Europe REST API - Publication endpoint
PubMed Central Europe REST API - Articles endpoint

This work is licensed under a Creative Commons Attribution 4.0 International License.