7OW6

HLA-A*11:01 presenting "VVVGADGVGK" to Alpha/Beta T cell receptor at 2.64Å 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 and alpha beta tcr

1. Beta 2 microglobulin

['B']

2. Class I alpha
HLA-A*11:01

['A']

3. Peptide
VVVGADGVGK

['C']

4. T cell receptor alpha
TRAV19

['D']

5. T cell receptor beta
TRBV6

['E']

Information on this structure on STCRdab.

Species

Homo sapiens (Human)

Locus / Allele group

HLA-A / HLA-A*11

Publication

Crystal structure of a TCR in complex with HLA-A*11:01 bound to KRAS G12D peptide (VVVGADGVGK)

Karuppiah, V., Robinson, R.A.

Structure deposition and release

Deposited: 2021-06-16

Released: 2022-07-20

Revised: 2022-10-12

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication

Peptide details

Length: Decamer (10 amino acids)

Sequence: VVVGADGVGK

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

GLU63

TRP167

MET5

TYR7

PHE33

TYR59

TYR171

TYR159

ARG163

P10 LYS

ASP77

ARG114

TYR84

TYR123

LYS146

THR143

ILE97

LEU81

ILE95

ASP74

TRP147

ASP116

THR80

P2 VAL

TYR7

TYR9

TYR99

TYR159

ARG163

MET45

ASN66

GLU63

VAL67

P3 VAL

GLN156

TYR9

TYR99

TYR159

ASN66

P4 GLY

ASN66

GLN70

GLN155

P5 ALA

GLN155

ALA69

GLN70

THR73

ASN66

P6 ASP

GLN70

THR73

ASP77

ARG114

GLN155

ILE97

TRP147

GLN156

P7 GLY

GLN155

P8 VAL

ALA150

LYS146

TRP147

P9 GLY

TRP147

THR73

ASP77

LYS146

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

ARG163

TRP167

TYR171

MET5

TYR59

GLU63

ASN66

TYR7

B Pocket

ALA24

VAL34

MET45

GLU63

ASN66

VAL67

TYR7

GLN70

TYR9

TYR99

C Pocket

GLN70

THR73

ASP74

TYR9

ILE97

D Pocket

ARG114

GLN155

GLN156

TYR159

LEU160

TYR99

E Pocket

ARG114

TRP147

ALA152

GLN156

ILE97

F Pocket

ASP116

TYR123

THR143

LYS146

TRP147

ASP77

THR80

LEU81

TYR84

ILE95

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-A11:01 IPD-IMGT/HLA* [ipd-imgt:HLA34732]	10 20 30 40 50 60 GSHSMRYFYTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW 70 80 90 100 110 120 DQETRNVKAQSQTDRVDLGTLRGYYNQSEDGSHTIQIMYGCDVGPDGRFLRGYRQDAYDG 130 140 150 160 170 180 KDYIALNEDLRSWTAADMAAQITKRKWEAAHAAEQQRAYLEGRCVEWLRRYLENGKETLQ 190 200 210 220 230 240 RTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT 250 260 270 FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

3. Peptide	VVVGADGVGK

4. T cell receptor alpha T cell receptor alpha TRAV19	10 20 30 40 50 60 AQKVTQAQTEISVVEKEDVTLDCVYETRDTAYYLFWYKQPPSGELVFLIRQPWWGEQNEI 70 80 90 100 110 120 SGRYSWNFQKSTSSFNFTITASQVVDSAVYFCAMSVPSGDGSYQFTFGKGTKLSVIPNIQ 130 140 150 160 170 180 NPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAV 190 200 AWSNKSDFACANAFNNSIIPEDT

5. T cell receptor beta T cell receptor beta TRBV6	10 20 30 40 50 60 MNAGVTQTPKFRVLKTGQSMTLLCAQDMNHEYMYWYRQDPGMGLRLIHYSVGEGTTAKGE 70 80 90 100 110 120 VPDGYNVSRLKKQNFLLGLESAAPSQTSVYFCASKVGPGQHNSPLHFGNGTRLTVTEDLN 130 140 150 160 170 180 KVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLK 190 200 210 220 230 240 EQPALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAE AWGRAD

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]

7OW6 assembly 1

Components

MHC Class I alpha chain [cif]

7OW6 assembly 1

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

7OW6 assembly 1

Peptide only [cif]

7OW6 assembly 1

Derived data

Data for this page [json]

https://api.histo.fyi/v1/structures/7ow6

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.