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1FO0

H2-Kb presenting "INFDFNTI" to Alpha/Beta T cell receptor at 2.50Å 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
['L']
2. Class I alpha
H2-Kb
['H']
3. Peptide
INFDFNTI
['P']
4. T cell receptor alpha
TRAV16
['A']
5. T cell receptor beta
TRBV1
['B']

Species


Locus / Allele group


Publication

Crystal structure of a T cell receptor bound to an allogeneic MHC molecule.

Reiser JB, Darnault C, Guimezanes A, Gr��goire C, Mosser T, Schmitt-Verhulst AM, Fontecilla-Camps JC, Malissen B, Housset D, Mazza G
Nat. Immunol. (2000) 1, 291-7 [doi:10.1038/79728]  [pubmed:11017099

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

Deposited: 2000-08-24
Released: 2000-10-02
Revised: 2017-02-01

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication


Peptide details

Length: Octamer (8 amino acids)

Sequence: INFDFNTI

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 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

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

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

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
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

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Complete structures

Aligned structures [cif]
  1. 1FO0 assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 1FO0 assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 1FO0 assembly 1  
Peptide only [cif]
  1. 1FO0 assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/1fo0

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