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3TJH

Truncated H2-Ld presenting "SPLDSLWWI" to Alpha/Beta T cell receptor at 2.12Å 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

Truncated class i with peptide and alpha beta tcr

1. Class I alpha
H2-Ld
['A']
2. Peptide
SPLDSLWWI
['B']
3. T cell receptor alpha
TRAV9
['C']
4. T cell receptor beta
TRBV13
['D']

Species


Locus / Allele group


Publication

T cell receptor signaling is limited by docking geometry to peptide-major histocompatibility complex.

Adams JJ, Narayanan S, Liu B, Birnbaum ME, Kruse AC, Bowerman NA, Chen W, Levin AM, Connolly JM, Zhu C, Kranz DM, Garcia KC
Immunity (2011) 35, 681-93 [doi:10.1016/j.immuni.2011.09.013]  [pubmed:22101157

T cell receptor (TCR) engagement of peptide-major histocompatibility complex (pMHC) is essential to adaptive immunity, but it is unknown whether TCR signaling responses are influenced by the binding topology of the TCR-peptide-MHC complex. We developed yeast-displayed pMHC libraries that enabled us to identify new peptide sequences reactive with a single TCR. Structural analysis showed that four peptides bound to the TCR with distinct 3D and 2D affinities using entirely different binding chemistries. Three of the peptides that shared a common docking mode, where key TCR-MHC germline interactions are preserved, induced TCR signaling. The fourth peptide failed to induce signaling and was recognized in a substantially different TCR-MHC binding mode that apparently exceeded geometric tolerances compatible with signaling. We suggest that the stereotypical TCR-MHC docking paradigm evolved from productive signaling geometries and that TCR signaling can be modulated by peptides that are recognized in alternative TCR-pMHC binding orientations.

Structure deposition and release

Deposited: 2011-08-24
Released: 2011-12-07
Revised: 2012-01-18

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: SPLDSLWWI

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 SER

TYR171
MET5
ARG62
TYR99
TYR159
TYR59
TYR7
ILE63
TRP167
P2 PRO

TYR99
TYR159
TYR7
ILE63
VAL66
TYR45
P3 LEU

TYR155
ARG97
VAL66
GLN70
GLU9
GLU114
TYR99
TYR156
TYR159
P4 ASP

TYR156
TYR155
GLN65
ARG97
VAL66
GLN70
P5 SER

GLU114
TYR156
GLN70
GLU9
TYR155
TRP73
ARG97
P6 LEU

TRP73
TYR156
TYR155
P7 TRP

TRP147
GLY151
TRP73
ALA150
ALA152
TYR156
TYR155
P8 TRP

VAL76
LYS146
THR143
ASN77
TRP147
TRP73
P9 ILE

LEU81
TYR123
LEU95
TRP73
LYS146
THR143
ASN77
ILE124
THR80
TRP147
TYR84
PHE116

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

THR24
PHE34
ARG45
ARG63
GLN66
VAL67
ARG7
GLY70
TYR9
MET99
C Pocket

GLY70
GLN73
TRP74
TYR9
GLN97
D Pocket

TYR114
GLU155
TYR156
ALA159
TYR160
MET99
E Pocket

TYR114
LYS147
GLY152
TYR156
GLN97
F Pocket

GLN116
ASP123
ILE143
ARG146
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. Class I alpha
H2-Ld
        10        20        30        40        50        60
MGPHSMRYYETATSRRGLGEPRYTSVGYVDDKEFVRFDSDAENPRYEPQVPWMEQEGPEY
        70        80        90       100       110       120
WERITQVAKGQEQWFRVNLRTLLGYYNQSAGGTHTLQRMYGCDVGSDGRLLRGYEQFAYD
       130       140       150       160       170
GCDYIALNEDLRTWTAADMAAQITRRKWEQAGAAEYYRAYLEGECVEWLHRYLKNGNATL

2. Peptide
SPLDSLWWI

3. T cell receptor alpha
T cell receptor alpha
TRAV9
        10        20        30        40        50        60
ADPGYLLEAQSVTQPDARVTVSEGASLQLRCKYSYSATPYLFWYVQYPRQGLQMLLKYYS
        70        80        90       100       110       120
GDPVVQGVNGFEAEFSKSDSSFHLRKASVHWSDSAVYFCAVSAKGTGSKLSFGKGAKLTV
       130       140       150       160       170       180
SPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFK
       190       200       210       220
SNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESSSRGGLEVLFQ

4. T cell receptor beta
T cell receptor beta
TRBV13
        10        20        30        40        50        60
ADPEAAVTQSPRNKVTVTGGNVTLSCRQTNSHNYMYWYRQDTGHGLRLIHYSYGAGNLQI
        70        80        90       100       110       120
GDVPDGYKATRTTQEDFFLLLELASPSQTSLYFCASSDAPGQLYFGEGSKLTVLEDLKNV
       130       140       150       160       170       180
FPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQ
       190       200       210       220       230       240
PALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAW
       250
GRADSRGGLEVLFQ


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. 3TJH assembly 1  

Components

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

Derived data

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

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