7N9J

H2-Db binding "YGFRNVVHI" at 1.74Å 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
H2-Db

['A']

3. Peptide
YGFRNVVHI

['C']

Species

Mus musculus (Mouse)

Locus / Allele group

H2-D / H2-Db

Publication

Structure of the complex between H2DB and melanoma HSF2 neoantigen YGFRNVVHI

Patskovsky, Y., Finnigan, J., Patskovska, L., Newman, J., Bhardwaj, N., Krogsgaard, M.

Structure deposition and release

Deposited: 2021-06-18

Released: 2022-06-22

Revised: 2022-06-22

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: YGFRNVVHI

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 TYR

TRP167

PHE33

MET5

TYR171

GLU163

GLU63

TYR59

LYS66

TYR159

TYR7

ARG62

P2 GLY

TYR159

GLU63

TYR7

LYS66

P3 PHE

LYS66

GLU9

TYR159

HIS155

TYR156

GLN70

P4 ARG

GLN72

GLY69

GLN65

GLN70

LYS66

P5 ASN

GLU9

PHE74

TYR156

GLN97

TRP73

PHE116

GLN70

P6 VAL

TRP73

HIS155

TYR156

P7 VAL

TYR156

TRP147

SER150

ALA152

HIS155

LYS146

TRP73

P8 HIS

ASN80

TRP147

SER77

LYS146

GLN72

TRP73

VAL76

THR143

P9 ILE

TRP73

TRP147

LEU81

TYR123

SER77

ILE124

ASN80

PHE116

LYS146

TYR84

LEU95

THR143

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

ALA159

GLY163

GLU167

ARG171

SER5

GLU59

ARG63

GLN66

ARG7

B Pocket

ILE24

PHE34

ARG45

ARG63

GLN66

LYS67

ARG7

GLY70

PHE9

MET99

C Pocket

GLY70

GLN73

TRP74

PHE9

GLN97

D Pocket

TYR114

GLU155

HIS156

ALA159

TYR160

MET99

E Pocket

TYR114

LYS147

GLY152

HIS156

GLN97

F Pocket

GLN116

ASP123

ILE143

ARG146

LYS147

VAL77

ARG80

ASN81

GLY84

THR95

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 H2-Db	10 20 30 40 50 60 MGPHSMRYFETAVSRPGLEEPRYISVGYVDNKEFVRFDSDAENPRYEPRAPWMEQEGPEY 70 80 90 100 110 120 WERETQKAKGQEQWFRVSLRNLLGYYNQSAGGSHTLQQMSGCDLGSDWRLLRGYLQFAYE 130 140 150 160 170 180 GRDYIALNEDLKTWTAADMAAQITRRKWEQSGAAEHYKAYLEGECVEWLHRYLKNGNATL 190 200 210 220 230 240 LRTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDG 250 260 270 280 TFQKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRWEPPPST

3. Peptide	YGFRNVVHI

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]

7N9J assembly 1

Components

MHC Class I alpha chain [cif]

7N9J assembly 1

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

7N9J assembly 1

Peptide only [cif]

7N9J assembly 1

Derived data

Data for this page [json]

https://api.histo.fyi/v1/structures/7n9j

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.