7NUI

HLA-B*08:01 binding "ELRSRYWAI" at 2.00Å 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']

2. Class I alpha
HLA-B*08:01

['A']

3. Peptide
ELRSRYWAI

['D']

Species

Homo sapiens (Human)

Locus / Allele group

HLA-B / HLA-B*08

Publication

Crystal structure of HLA-B*08:01 in complex with ELRSRYWAI viral peptide

Mavridis, G.

Structure deposition and release

Deposited: 2021-03-12

Released: 2021-04-14

Revised: 2021-04-14

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: ELRSRYWAI

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 GLU

TYR171

TRP167

TYR99

TYR159

TYR59

TYR7

ARG62

THR163

ASN63

MET5

ILE66

P2 LEU

ILE66

PHE67

TYR99

TYR159

TYR7

SER24

ASN63

ASN70

PHE36

P3 ARG

ILE66

TYR116

ASN70

ASP156

ASN114

TYR99

TYR159

P4 SER

ASN70

ILE66

P5 ARG

SER24

TYR116

THR69

ASN70

THR71

ASP9

TYR99

ASP74

THR73

P6 TYR

THR73

THR69

P7 TRP

VAL152

GLN155

THR73

TRP147

ALA150

SER77

P8 ALA

THR143

LYS146

THR73

SER77

ASN80

TRP147

GLU76

P9 ILE

THR143

LYS146

LEU95

TYR123

ILE124

TYR84

ASN80

LEU81

TRP147

SER77

TYR116

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

MET5

TYR59

ASN63

ILE66

TYR7

B Pocket

SER24

VAL34

MET45

ASN63

ILE66

PHE67

TYR7

ASN70

ASP9

TYR99

C Pocket

ASN70

THR73

ASP74

ASP9

SER97

D Pocket

ASN114

GLN155

ASP156

TYR159

LEU160

TYR99

E Pocket

ASN114

TRP147

VAL152

ASP156

SER97

F Pocket

TYR116

TYR123

THR143

LYS146

TRP147

SER77

ASN80

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-B08:01 IPD-IMGT/HLA* [ipd-imgt:HLA34671]	10 20 30 40 50 60 GSHSMRYFDTAMSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRMEPRAPWIEQEGPEYW 70 80 90 100 110 120 DRNTQIFKTNTQTDRESLRNLRGYYNQSEAGSHTLQSMYGCDVGPDGRLLRGHNQYAYDG 130 140 150 160 170 180 KDYIALNEDLRSWTAADTAAQITQRKWEAARVAEQDRAYLEGTCVEWLRRYLENGKDTLE 190 200 210 220 230 240 RADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT 250 260 270 FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

3. Peptide	ELRSRYWAI

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]

7NUI assembly 1

Components

MHC Class I alpha chain [cif]

7NUI assembly 1

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

7NUI assembly 1

Peptide only [cif]

7NUI assembly 1

Derived data

Data for this page [json]

https://api.histo.fyi/v1/structures/7nui

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.