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7PB2

HLA-A*11:01 presenting "VVVGADGVGK" to Alpha/Beta T cell receptor at 3.41Å 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.

Information sections

Complex type

Class i with peptide and alpha beta tcr

1. Beta 2 microglobulin
['B', 'G']
2. Class I alpha
HLA-A*11:01
['A', 'F']
3. Peptide
VVVGADGVGK
['C', 'H']
4. T cell receptor alpha
TRAV19
['D']
5. T cell receptor beta
TRBV6
['E']

Species

Locus / Allele group

HLA-A / HLA-A*11

Publication

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

Coles, C.H., Karuppiah, V., Robinson, R.A.

Structure deposition and release

Deposited: 2021-07-30
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

MET5
GLU63
TYR59
TYR171
TYR7
TYR99
TYR159
ARG163
TRP167
 P10 LYS

ILE95
TRP147
THR143
ASP116
TYR123
ILE97
LEU81
ASP74
THR80
LYS146
ASP77
ARG114
TYR84
 P2 VAL

TYR99
ARG163
TYR9
ASN66
GLU63
VAL67
TYR159
TYR7
MET45
 P3 VAL

TYR99
TYR159
GLN155
ARG114
GLN156
TYR9
ASN66
GLN70
 P4 GLY

GLN155
GLN70
GLN156
ASN66
 P5 ALA

ALA69
GLN155
ASN66
GLN70
 P6 ASP

GLN155
ILE97
GLN70
TRP147
GLN156
ASP116
THR73
ARG114
 P7 GLY

GLN155
 P8 VAL

LYS146
TRP147
ALA150
 P9 GLY

THR73
ASP77
TRP147
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-A*11:01
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
AQKVTQAQTEISVVEKEDVTLDCVYETRDTTYYLFWYKQPPSGELVFLIRRNSFDEQNEI
        70        80        90       100       110       120
SGRYSWNFQKSTSSFNFTITASQVVDSAVYFCALSGPSGAGSYQLTFGKGTKLSVIPNIQ
       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
NAGVTQTPKFRVLKTGQSMTLLCAQDMNHEYMYWYRQDPGMGLRLIHYSVGEGTTAKGEV
        70        80        90       100       110       120
PDGYNVSRLKKQNFLLGLESAAPSQTSVYFCASSYGPGQHNSPLHFGNGTRLTVTEDLNK
       130       140       150       160       170       180
VFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKE
       190       200       210       220       230       240
QPALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEA

WGRAD

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

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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]
  1. 7PB2 assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 7PB2 assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 7PB2 assembly 1  
Peptide only [cif]
  1. 7PB2 assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/7pb2

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


Creative Commons Licence
This work is licensed under a Creative Commons Attribution 4.0 International License.