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6ULR

HLA-C*08:02 presenting "GADGVGKSA" to Alpha/Beta T cell receptor at 3.20Å 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']
2. Class I alpha
HLA-C*08:02
['A']
3. Peptide
GADGVGKSA
['C']
4. T cell receptor alpha
TRAV4
['D']
5. T cell receptor beta
TRBV5
['E']

Species

Locus / Allele group

HLA-C / HLA-C*08

Publication

High-affinity oligoclonal TCRs define effective adoptive T cell therapy targeting mutant KRAS-G12D.

Sim MJW, Lu J, Spencer M, Hopkins F, Tran E, Rosenberg SA, Long EO, Sun PD
Proc. Natl. Acad. Sci. U.S.A. (2020) [doi:10.1073/pnas.1921964117]  [pubmed:32461371] 

Structure deposition and release

Deposited: 2019-10-08
Released: 2020-05-27
Revised: 2020-06-17

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: GADGVGKSA

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 GLY

TYR59
TYR7
GLU63
LYS66
MET5
TRP167
TYR171
PHE33
TYR99
TYR159
 P2 ALA

TYR9
TYR99
TYR159
TYR7
GLU63
LYS66
TYR67
 P3 ASP

ARG97
TYR9
ARG156
LYS66
GLN70
TYR99
TYR159
 P4 GLY

GLN70
TYR159
LYS66
ARG97
ARG156
 P5 VAL

ARG69
ARG156
THR73
GLN70
LYS66
 P6 GLY

THR73
GLU152
GLN70
ARG156
 P7 LYS

THR73
ALA150
LYS146
GLU152
TRP147
ARG156
 P8 SER

THR73
VAL76
SER77
LYS146
ASN80
TRP147
 P9 ALA

LEU81
SER77
TRP147
THR143
ASN80
TYR84
TYR123
VAL76
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
THR163
TRP167
TYR171
MET5
TYR59
GLU63
LYS66
TYR7
B Pocket

ALA24
VAL34
GLY45
GLU63
LYS66
TYR67
TYR7
GLN70
TYR9
TYR99
C Pocket

GLN70
THR73
ASP74
TYR9
ARG97
D Pocket

ASN114
GLN155
ARG156
TYR159
LEU160
TYR99
E Pocket

ASN114
TRP147
GLU152
ARG156
ARG97
F Pocket

PHE116
TYR123
THR143
LYS146
TRP147
SER77
ASN80
LEU81
TYR84
LEU95

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
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
        70        80        90
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM
2. Class I alpha
HLA-C*08:02
IPD-IMGT/HLA
[ipd-imgt:HLA35375]
        10        20        30        40        50        60
CSHSMRYFYTAVSRPGRGEPRFIAVGYVDDTQFVQFDSDAASPRGEPRAPWVEQEGPEYW
        70        80        90       100       110       120
DRETQKYKRQAQTDRVSLRNLRGYYNQSEAGSHTLQRMYGCDLGPDGRLLRGYNQFAYDG
       130       140       150       160       170       180
KDYIALNEDLRSWTAADKAAQITQRKWEAAREAEQRRAYLEGTCVEWLRRYLENGKKTLQ
       190       200       210       220       230       240
RAEHPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
       250       260       270
FQKWAAVVVPSGEEQRYTCHVQHEGLPEPLTLRW
3. Peptide
GADGVGKSA
4. T cell receptor alpha
T cell receptor alpha
TRAV4
        10        20        30        40        50        60
MAGLAKTTQPISVDSYEGQEVNITCSHNNIATNDYITWYQQFPSQGPRFIIQGYKTKVTN
        70        80        90       100       110       120
EVASLFIPADRKSSTLSLPRVSLSDTAVYYCLVGDMDQAGTALIFGKGTTLSVSSDIQNP
       130       140       150       160       170       180
DPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAW
       190       200
SNKSDFACANAFNNSIIPEDTFFPSP
5. T cell receptor beta
T cell receptor beta
TRBV5
        10        20        30        40        50        60
MAGVTQSPTHLIKTRGQQVTLRCSPKSGHDTVSWYQQALGQGPQFIFQYYEEEERQRGNF
        70        80        90       100       110       120
PDRFSGHQFPNYSSELNVNALLLGDSALYLCASSLGEGRVDGYTFGSGTRLTVVEDLRNV
       130       140       150       160       170       180
FPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQ
       190       200       210       220       230       240
PALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAW

GRAD

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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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. 6ULR assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 6ULR assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 6ULR assembly 1  
Peptide only [cif]
  1. 6ULR assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/6ulr

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.