8D5J

H2-Kd binding "KYLQVASHV" at 1.95Å 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-Kd

['A']

3. Peptide
KYLQVASHV

['C']

Species

Mus musculus (Mouse)

Locus / Allele group

H2-K / H2-Kd

Publication

The complex of Pre-mRNA-Processing Factor 19 (Prpf19) neoantigen KYLQVASHV Presented by H2-Kd

Custodio, J.M.F., Baker, B.M.

Structure deposition and release

Deposited: 2022-06-04

Released: 2022-07-06

Revised: 2022-07-06

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: KYLQVASHV

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 LYS

GLU62

GLU163

PHE99

TYR59

TYR159

TYR7

ARG66

GLN63

TRP167

LEU5

TYR171

P2 TYR

TYR159

TYR7

VAL9

ARG66

GLN63

PHE45

ALA24

ARG97

ALA67

PHE74

PHE22

GLU163

ASP70

PHE99

P3 LEU

PHE99

TYR159

ARG66

GLN114

TYR155

TYR156

ARG97

GLU163

ASP70

P4 GLN

TYR156

SER69

ARG97

ARG66

ASP70

TYR155

P5 VAL

ASP70

TYR155

PHE74

TYR156

ARG97

PHE116

TRP147

TRP73

P6 ALA

TYR156

ASP152

TYR155

P7 SER

ASP152

TRP147

TYR156

ALA150

TRP73

P8 HIS

TRP147

TRP73

VAL76

LYS146

GLN72

THR143

P9 VAL

LYS146

THR143

ILE142

THR80

ALA81

TRP147

TRP73

TYR84

SER77

PHE95

TYR123

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

GLU63

GLN66

ARG7

B Pocket

ILE24

PHE34

ARG45

GLU63

GLN66

ARG67

ARG7

SER70

PHE9

MET99

C Pocket

SER70

GLN73

TRP74

PHE9

GLN97

D Pocket

TYR114

GLU155

TYR156

ALA159

TYR160

MET99

E Pocket

TYR114

LYS147

GLY152

TYR156

GLN97

F Pocket

GLN116

ASP123

ILE143

ARG146

LYS147

VAL77

ARG80

THR81

ARG84

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 MIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKD 70 80 90 WSFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

2. Class I alpha H2-Kd	10 20 30 40 50 60 MGPHSLRYFVTAVSRPGLGEPRFIAVGYVDDTQFVRFDSDADNPRFEPRAPWMEQEGPEY 70 80 90 100 110 120 WEEQTQRAKSDEQWFRVSLRTAQRYYNQSKGGSHTFQRMFGCDVGSDWRLLRGYQQFAYD 130 140 150 160 170 180 GRDYIALNEDLKTWTAADTAALITRRKWEQAGDAEYYRAYLEGECVEWLRRYLELGNETL 190 200 210 220 230 240 LRTDSPKAHVTYHPRSQVDVTLRCWALGFYPADITLTWQLNGEDLTQDMELVETRPAGDG 250 260 270 TFQKWAAVVVPLGKEQNYTCHVHHKGLPEPLTLRWE

3. Peptide	KYLQVASHV

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]

8D5J assembly 1

Components

MHC Class I alpha chain [cif]

8D5J assembly 1

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

8D5J assembly 1

Peptide only [cif]

8D5J assembly 1

Derived data

Data for this page [json]

https://api.histo.fyi/v1/structures/8d5j

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.