H2-Kb presenting "INFDFNTI" to Alpha/Beta T cell receptor at 2.50Å 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
H2-Kb
INFDFNTI
TRAV16
TRBV1
Species
Locus / Allele group
Crystal structure of a T cell receptor bound to an allogeneic MHC molecule.
Transformation acoustics, as an unconventional theory, provides a powerful tool to design various kinds of acoustic devices with excellent functionalities. However, the required ideal parameters, which are prescribed by the method, are both complex and hard to implement-even using acoustic metamaterials. Furthermore, simplified parameter materials are generally favored in transformation-acoustic design due to its easier realization with artificial structures. In this letter, we propose a coordinate transformation methodology for achieving simplified parameters by tuning the impedance distribution in the geometric limit, where the transformation media parameters can be derived by setting tunable impedance functions in the original space and a combination of suitable linear or nonlinear coordinate transformation. Based on this approach, both two-dimensional acoustic cloak and concentrators are designed with different sets of simplified parameters. Numerical simulations indicate good performance of these devices with minimized scattering at higher frequencies. The proposed method provides more opportunities to realize the designed acoustic devices experimentally, and can also be used for other transformation-acoustic designs including 3D cases.
Structure deposition and release
Data provenance
Publication data retrieved from PDBe REST API8 and PMCe REST API9
Other structures from this publication
![](https://images.histo.fyi/cleft/side/combined/1fo0_1_combined_medium.png)
![](https://images.histo.fyi/cleft/yrb/1fo0_1_yrb_medium.png)
![](https://images.histo.fyi/cleft/top/combined/1fo0_1_combined_medium.png)
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
ILE
TYR171
TRP167
LEU5
TYR159
TYR59
TYR7
THR163
GLU63
LYS66
|
P2
ASN
ASN70
TYR45
GLU63
LYS66
VAL9
SER99
GLU24
TYR159
TYR7
|
P3
PHE
ARG155
GLU152
ASN70
LYS66
GLN114
LEU156
SER99
TYR159
|
P4
ASP
GLU152
ASN70
LYS66
ARG155
|
P5
PHE
ASN70
ARG155
GLN114
VAL9
PHE74
VAL97
TYR116
SER73
SER99
|
P6
ASN
TRP147
TYR116
SER73
ASP77
ARG155
GLU152
|
P7
THR
TRP147
SER73
VAL76
LYS146
ASP77
|
P8
ILE
THR80
TYR84
THR143
TYR123
LYS146
TRP147
TYR116
LEU81
ASP77
ILE95
|
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]
![](https://images.histo.fyi/cleft/pockets/labelled/1fo0_1_labelled_medium.png)
![](https://images.histo.fyi/cleft/terminii/labelled/1fo0_1_labelled_medium.png)
A Pocket
ALA159
GLY163
GLU167
ARG171
SER5
GLU59
ARG63
GLN66
ARG7
|
B Pocket
MET24
PHE34
ARG45
ARG63
GLN66
LYS67
ARG7
GLY70
PHE9
ILE99
|
C Pocket
GLY70
GLN73
SER74
PHE9
GLN97
|
D Pocket
TYR114
GLU155
ARG156
ALA159
TYR160
ILE99
|
E Pocket
TYR114
LYS147
GLY152
ARG156
GLN97
|
F Pocket
GLN116
ASP123
ILE143
HIS146
LYS147
VAL77
ARG80
THR81
GLY84
THR95
|
Colour key
Data provenance
1. Beta 2 microglobulin
Beta 2 microglobulin
|
10 20 30 40 50 60
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW 70 80 90 SFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM |
2. Class I alpha
H2-Kb
|
10 20 30 40 50 60
MGPHSLRYFVTAVSRPGLGEPRYMEVGYVDDTEFVRFDSDAENPRYEPRARWMEQEGPEY 70 80 90 100 110 120 WERETQKAKGNEQSFRVDLRTLLGYYNQSKGGSHTIQVISGCEVGSDGRLLRGYQQYAYD 130 140 150 160 170 180 GCDYIALNEDLKTWTAADMAALITKHKWEQAGEAERLRAYLEGTCVEWLRRYLKNGNATL 190 200 210 220 230 240 LRTDSPKAHVTHHSRPEDKVTLRCWALGFYPADITLTWQLNGEELIQDMELVETRPAGDG 250 260 270 TFQKWASVVVPLGKEQYYTCHVYHQGLPEPLTLRWE |
3. Peptide
|
INFDFNTI
|
4. T cell receptor alpha
T cell receptor alpha
TRAV16
|
10 20 30 40 50 60
QKVTQTQTSISVMEKTTVTMDCVYETQDSSYFLFWYKQTASGEIVFLIRQDSYKKENATV 70 80 90 100 110 GHYSLNFQKPKSSIGLIITATQIEDSAVYFCAMRGDYGGSGNKLIFGTGTLLSVKP |
5. T cell receptor beta
T cell receptor beta
TRBV1
|
10 20 30 40 50 60
VTLLEQNPRWRLVPRGQAVNLRCILKNSQYPWMSWYQQDLQKQLQWLFTLRSPGDKEVKS 70 80 90 100 110 LPGADYLATRVTDTELRLQVANMSQGRTLYCTCSADRVGNTLYFGEGSRLIV |
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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This work is licensed under a Creative Commons Attribution 4.0 International License.