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7RRG

HLA-A*03:01 presenting "ALHGGWTTK" to Alpha/Beta T cell receptor at 2.12Å 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-A*03:01
['A']
3. Peptide
ALHGGWTTK
['C']
4. T cell receptor alpha
TRAV4
['D']
5. T cell receptor beta
TRBV11
['E']

Species


Locus / Allele group


Publication

Immunogenicity and therapeutic targeting of a public neoantigen derived from mutated PIK3CA.

Chandran, S.S., Ma, J., Klatt, M.G., Dundar, F., Bandlamudi, C., Razavi, P., Wen, H.Y., Weigelt, B., Zumbo, P., Fu, S.N., Banks, L.B., Yi, F., Vercher, E., Etxeberria, I., Bestman, W.D., Da Cruz Paula, A., Aricescu, I.S., Drilon, A., Betel, D., Scheinberg, D.A., Baker, B.M., Klebanoff, C.A.
(2022) 28, 946-957 [doi:10.1038/s41591-022-01786-3]  [pubmed:35484264

Public neoantigens (NeoAgs) represent an elite class of shared cancer-specific epitopes derived from recurrently mutated driver genes. Here we describe a high-throughput platform combining single-cell transcriptomic and T cell receptor (TCR) sequencing to establish whether mutant PIK3CA, among the most frequently genomically altered driver oncogenes, generates an immunogenic public NeoAg. Using this strategy, we developed a panel of TCRs that recognize an endogenously processed neopeptide encompassing a common PIK3CA hotspot mutation restricted by the prevalent human leukocyte antigen (HLA)-A*03:01 allele. Mechanistically, immunogenicity to this public NeoAg arises from enhanced neopeptide/HLA complex stability caused by a preferred HLA anchor substitution. Structural studies indicated that the HLA-bound neopeptide presents a comparatively 'featureless' surface dominated by the peptide's backbone. To bind this epitope with high specificity and affinity, we discovered that a lead TCR clinical candidate engages the neopeptide through an extended interface facilitated by an unusually long CDR3β loop. In patients with diverse malignancies, we observed NeoAg clonal conservation and spontaneous immunogenicity to the neoepitope. Finally, adoptive transfer of TCR-engineered T cells led to tumor regression in vivo in mice bearing PIK3CA-mutant tumors but not wild-type PIK3CA tumors. Together, these findings establish the immunogenicity and therapeutic potential of a mutant PIK3CA-derived public NeoAg.

Structure deposition and release

Deposited: 2021-08-09
Released: 2022-03-23
Revised: 2022-06-01

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: ALHGGWTTK

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 ALA

MET5
TYR159
GLN62
GLU63
TYR7
TRP167
TYR59
TYR171
P2 LEU

TYR99
VAL67
TYR159
TYR7
MET45
PHE9
ASN66
GLU63
P3 HIS

TYR159
GLN70
TYR99
ASN66
ARG114
GLN155
LEU156
P4 GLY

ASN66
GLN155
P5 GLY

GLU152
GLN155
P6 TRP

ARG114
GLU152
THR73
LEU156
TRP147
ALA153
TRP133
P7 THR

ALA150
THR73
ASP77
TRP147
GLU152
LYS146
P8 THR

THR73
VAL76
ASP77
TRP147
LYS146
P9 LYS

ARG114
LYS146
ILE97
ILE95
TYR84
THR143
TYR123
ASP77
TRP147
THR80
ASP116
ILE124
ILE142
LEU81

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
ASN66
TYR7
B Pocket

ALA24
VAL34
MET45
GLU63
ASN66
VAL67
TYR7
GLN70
PHE9
TYR99
C Pocket

GLN70
THR73
ASP74
PHE9
ILE97
D Pocket

ARG114
GLN155
LEU156
TYR159
LEU160
TYR99
E Pocket

ARG114
TRP147
GLU152
LEU156
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*03:01
IPD-IMGT/HLA
[ipd-imgt:HLA34773]
        10        20        30        40        50        60
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
        70        80        90       100       110       120
DQETRNVKAQSQTDRVDLGTLRGYYNQSEAGSHTIQIMYGCDVGSDGRFLRGYRQDAYDG
       130       140       150       160       170       180
KDYIALNEDLRSWTAADMAAQITKRKWEAAHEAEQLRAYLDGTCVEWLRRYLENGKETLQ
       190       200       210       220       230       240
RTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
       250       260       270
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRW

3. Peptide
ALHGGWTTK

4. T cell receptor alpha
T cell receptor alpha
TRAV4
        10        20        30        40        50        60
MLAKTTQPISMDSYEGQEVNITCSHNNIATNDYITWYQQFPSQGPRFIIQGYKTKVTNEV
        70        80        90       100       110       120
ASLFIPADRKSSTLSLPRVSLSDTAVYYCLVGGAYTGGFKTIFGAGTRLFVKANIQNPDP
       130       140       150       160       170       180
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
       190       200
KSDFACANAFNNSIIPEDTFFPSPESS

5. T cell receptor beta
T cell receptor beta
TRBV11
        10        20        30        40        50        60
MEAGVAQSPRYKIIEKRQSVAFWCNPISGHATLYWYQQILGQGPKLLIQFQNNGVVDDSQ
        70        80        90       100       110       120
LPKDRFSAERLKGVDSTLKIQPAKLEDSAVYLCASSLVAETYEQYFGPGTRLTVTEDLNK
       130       140       150       160       170       180
VFPPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVCTDPQPLKE
       190       200       210       220       230       240
QPALNDSRYSLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEA

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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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. 7RRG assembly 1  

Components

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

Derived data

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

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