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3UTT

HLA-A*02:01 presenting "ALWGPDPAAA" to Alpha/Beta T cell receptor at 2.60Å 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*02:01
['A', 'F']
3. Peptide
ALWGPDPAAA
['C', 'H']
4. T cell receptor alpha
TRAV12
['D']
5. T cell receptor beta
TRBV12
['E']

Species


Locus / Allele group


Publication

Structural basis for the killing of human beta cells by CD8(+) T cells in type 1 diabetes.

Bulek AM, Cole DK, Skowera A, Dolton G, Gras S, Madura F, Fuller A, Miles JJ, Gostick E, Price DA, Drijfhout JW, Knight RR, Huang GC, Lissin N, Molloy PE, Wooldridge L, Jakobsen BK, Rossjohn J, Peakman M, Rizkallah PJ, Sewell AK
Nat. Immunol. (2012) 13, 283-9 [doi:10.1038/ni.2206]  [pubmed:22245737

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

Deposited: 2011-11-26
Released: 2012-01-25
Revised: 2019-07-17

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: ALWGPDPAAA

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

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

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
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

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*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

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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. 3UTT assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 3UTT assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 3UTT assembly 1  
Peptide only [cif]
  1. 3UTT assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/3utt

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