HLA-A*02:01 presenting "ALWGPDPAAA" to Alpha/Beta T cell receptor at 2.60Å resolution
Data provenance
Information sections
- Publication
- Peptide details
- Peptide neighbours
- Binding cleft pockets
- Chain sequences
- Downloadable data
- Data license
- Footnotes
Complex type
Class i with peptide and alpha beta tcr
HLA-A*02:01
ALWGPDPAAA
TRAV12
TRBV12
Species
Locus / Allele group
Structural basis for the killing of human beta cells by CD8(+) T cells in type 1 diabetes.
In this study, we demonstrate three-dimensional (3D) hollow nanosphere electrocatalysts for CO2 conversion into formate with excellent H-Cell performance and industrially-relevant current density in a 25 cm2 membrane electrode assembly electrolyzer device. Varying calcination temperature maximized formate production via optimizing the crystallinity and particle size of the constituent SnO2 nanoparticles. The best performing SnO2 nanosphere catalysts contained ~ 7.5 nm nanocrystals and produced 71-81% formate Faradaic efficiency (FE) between -0.9 V and -1.3 V vs. the reversible hydrogen electrode (RHE) at a maximum formate partial current density of 73 ± 2 mA cmgeo-2 at -1.3 V vs. RHE. The higher performance of nanosphere catalysts over SnO2 nanoparticles and commercially-available catalyst could be ascribed to their initial structure providing higher electrochemical surface area and preventing extensive nanocrystal growth during CO2 reduction. Our results are among the highest performance reported for SnO2 electrocatalysts in aqueous H-cells. We observed an average 68 ± 8% FE over 35 h of operation with multiple on/off cycles. In situ Raman and time-dependent X-ray diffraction measurements identified metallic Sn as electrocatalytic active sites during long-term operation. Further evaluation in a 25 cm2 electrolyzer cell demonstrated impressive performance with a sustained current density of 500 mA cmgeo-2 and an average 75 ± 6% formate FE over 24 h of operation. Our results provide additional design concepts for boosting the performance of formate-producing catalysts.
Structure deposition and release
Data provenance
Publication data retrieved from PDBe REST API8 and PMCe REST API9
Other structures from this publication



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
TRP167
TYR59
TYR171
TYR159
TYR7
LYS66
GLU63
MET5
|
P10
ALA
TYR123
LYS146
TRP147
TYR116
LEU81
THR73
ASP77
THR80
THR143
TYR84
|
P2
LEU
TYR159
TYR7
MET45
LYS66
GLU63
HIS70
PHE9
VAL67
TYR99
|
P3
TRP
TYR99
GLN155
TYR159
HIS70
HIS114
LYS66
VAL152
LEU156
ARG97
|
P4
GLY
GLN155
LYS66
|
P5
PRO
LYS66
ALA69
|
P6
ASP
LYS66
ALA69
THR73
HIS70
|
P7
PRO
THR73
HIS70
ARG97
|
P8
ALA
VAL152
ARG97
TRP147
THR73
ASP77
|
P9
ALA
VAL76
THR143
LYS146
TRP147
THR73
ASP77
|
Colour key
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]


A Pocket
TYR159
THR163
TRP167
TYR171
MET5
TYR59
GLU63
LYS66
TYR7
|
B Pocket
ALA24
VAL34
MET45
GLU63
LYS66
VAL67
TYR7
HIS70
PHE9
TYR99
|
C Pocket
HIS70
THR73
HIS74
PHE9
ARG97
|
D Pocket
HIS114
GLN155
LEU156
TYR159
LEU160
TYR99
|
E Pocket
HIS114
TRP147
VAL152
LEU156
ARG97
|
F Pocket
TYR116
TYR123
THR143
LYS146
TRP147
ASP77
THR80
LEU81
TYR84
VAL95
|
Colour key
Data provenance
1. Beta 2 microglobulin
Beta 2 microglobulin
|
10 20 30 40 50 60
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD 70 80 90 WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM |
2. Class I alpha
HLA-A*02:01
IPD-IMGT/HLA
[ipd-imgt:HLA35266] |
10 20 30 40 50 60
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW 70 80 90 100 110 120 DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG 130 140 150 160 170 180 KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ 190 200 210 220 230 240 RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT 250 260 270 FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE |
3. Peptide
|
ALWGPDPAAA
|
4. T cell receptor alpha
T cell receptor alpha
TRAV12
|
10 20 30 40 50 60
EVEQDPGPLSVPEGAIVSLNCTYSNSAFQYFMWYRQYSRKGPELLMYTYSSGNKEDGRFT 70 80 90 100 110 120 AQVDKSSKYISLFIRDSQPSDSATYLCAMRGDSSYKLIFGSGTRLLVRPDIQNPDPAVYQ 130 140 150 160 170 180 LRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDF 190 ACANAFNNSIIPEDTFFPS |
5. T cell receptor beta
T cell receptor beta
TRBV12
|
10 20 30 40 50 60
AGVIQSPRHEVTEMGQQVTLRCKPISGHDYLFWYRQTMMRGLELLIYFNNNVPIDDSGMP 70 80 90 100 110 120 EDRFSAKMPNASFSTLKIQPSEPRDSAVYFCASSLWEKLAKNIQYFGAGTRLSVLEDLKN 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
Components
Data license
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

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