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6UZ1

HLA-A*02:01 presenting "LLFGYPVYV" to Alpha/Beta T cell receptor at 3.14Å 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
LLFGYPVYV
['C', 'H']
4. T cell receptor alpha
TRAV12
['I']
5. T cell receptor beta
TRBV6
['J']

Species


Locus / Allele group


Publication

An Engineered T Cell Receptor Variant Realizes the Limits of Functional Binding Modes.

Singh NK, Alonso JA, Harris DT, Anderson SD, Ma J, Hellman LM, Rosenberg AM, Kolawole EM, Evavold BD, Kranz DM, Baker BM
Biochemistry (2020) [doi:10.1021/acs.biochem.0c00689]  [pubmed:33074657

T cell receptors (TCRs) orchestrate cellular immunity by recognizing peptides presented by a range of major histocompatibility complex (MHC) proteins. Naturally occurring TCRs bind the composite peptide/MHC surface, recognizing peptides that are structurally and chemically compatible with the TCR binding site. Here we describe a molecularly evolved TCR variant that binds the human class I MHC protein HLA-A2 independent of the bound peptide, achieved by a drastic perturbation of the TCR binding geometry that places the molecule far from the peptide binding groove. This unique geometry is unsupportive of normal T cell signaling. A substantial divergence between affinity measurements in solution and in two dimensions between proximal cell membranes leads us to attribute the lack of signaling to steric hindrance that limits binding in the confines of a cell-cell interface. Our results provide an example of how receptor binding geometry can impact T cell function and provide further support for the view that germline-encoded residues in TCR binding loops evolved to drive productive TCR recognition and signaling.

Structure deposition and release

Deposited: 2019-11-14
Released: 2020-10-28
Revised: 2020-11-11

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: LLFGYPVYV

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 LEU

TYR171
TYR159
TYR59
TYR7
GLU63
LYS66
MET5
THR163
TRP167
P2 LEU

GLU63
LYS66
TYR159
VAL67
PHE9
TYR7
MET45
HIS70
TYR99
P3 PHE

ARG97
HIS70
TYR99
LYS66
GLN155
LEU156
TYR159
P4 GLY

LYS66
P5 TYR

VAL152
GLN155
ALA150
P6 PRO

THR73
P7 VAL

VAL152
TRP147
THR73
ARG97
TYR116
ASP77
P8 TYR

GLN72
THR73
THR143
LYS146
TRP147
ASP77
VAL76
P9 VAL

THR80
TYR84
TYR123
THR143
LYS146
TYR116
LEU81
TRP147
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
LLFGYPVYV

4. T cell receptor alpha
T cell receptor alpha
TRAV12
        10        20        30        40        50        60
EVEQNSGPLSVPEGAIASLNCTYSIRSSTSFFWYRQYSGKSPELIMSIYSNGDKEDGRFT
        70        80        90       100
AQLNKASQYVSLLIRDSQPSDSATYLCAVTTDRSGKLQFGAGTQVVVTPD

5. T cell receptor beta
T cell receptor beta
TRBV6
        10        20        30        40        50        60
AGVTQTPKFQVLKTGQSMTLQCAQDMNHEYMAWYRQDPGMGLRLIHYSVGVGITDQGDVP
        70        80        90       100       110
DGYKVSRSTTEDFPLRLLSAAPSQTSVYFCASRPGAAGGRPELYFGPGTRLTVTE


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. 6UZ1 assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 6UZ1 assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 6UZ1 assembly 1  
Peptide only [cif]
  1. 6UZ1 assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/6uz1

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