8D5F

H2-Dd binding "TGAARFDEF" at 2.31Å 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-Dd

['A']

3. Peptide
TGAARFDEF

['P']

Species

Mus musculus (Mouse)

Locus / Allele group

H2-D / H2-Dd

Publication

The complex of Gtf2b neoantigen TGAARFDEF 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: TGAARFDEF

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 THR

GLU63

TRP167

LEU5

TYR171

TYR159

ARG62

TYR59

TYR7

GLU163

ARG66

P2 GLY

TYR7

GLU163

ARG66

GLU63

TYR159

P3 ALA

TRP97

TYR159

TYR7

ASN70

ALA99

ARG66

TRP114

GLU24

P4 ALA

ARG66

TRP114

TRP97

ASN70

P5 ARG

SER73

ASP77

PHE74

PHE116

ASN70

TRP147

TRP114

TRP97

P6 PHE

ARG155

P7 ASP

TRP147

ASP77

ALA150

ALA152

ARG155

P8 GLU

TRP147

ASP77

VAL76

LYS146

THR143

THR80

P9 PHE

THR80

TYR84

TRP147

ASP77

PHE116

TYR123

LEU95

LYS146

THR143

ILE142

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

LEU159

CYS163

LEU167

LEU171

ARG5

TRP59

THR63

ALA66

PHE7

B Pocket

VAL24

ARG34

GLU45

THR63

ALA66

LYS67

PHE7

GLU70

THR9

GLY99

C Pocket

GLU70

PHE73

ARG74

THR9

MET97

D Pocket

GLN114

ASP155

ARG156

LEU159

GLU160

GLY99

E Pocket

GLN114

GLU147

ALA152

ARG156

MET97

F Pocket

ALA116

ILE123

ARG143

TRP146

GLU147

LEU77

ALA80

LEU81

TYR84

GLN95

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 WSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM

2. Class I alpha H2-Dd	10 20 30 40 50 60 SHSLRYFVTAVSRPGFGEPRYMEVGYVDNTEFVRFDSDAENPRYEPRARWIEQEGPEYWE 70 80 90 100 110 120 RETRRAKGNEQSFRVDLRTALRYYNQSAGGSHTLQWMAGCDVESDGRLLRGYWQFAYDGC 130 140 150 160 170 180 DYIALNEDLKTWTAADMAAQITRRKWEQAGAAERDRAYLEGECVEWLRRYLKNGNATLLR 190 200 210 220 230 240 TDPPKAHVTHHRRPEGDVTLRCWALGFYPADITLTWQLNGEELTQEMELVETRPAGDGTF 250 260 270 QKWASVVVPLGKEQKYTCHVEHEGLPEPLTLRWG

3. Peptide	TGAARFDEF

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]

8D5F assembly 1

Components

MHC Class I alpha chain [cif]

8D5F assembly 1

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

8D5F assembly 1

Peptide only [cif]

8D5F assembly 1

Derived data

Data for this page [json]

https://api.histo.fyi/v1/structures/8d5f

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.