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3BUY

H2-Db binding "LSLRNPILV" 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

1. Beta 2 microglobulin
['B']
2. Class I alpha
H2-Db
['A']
3. Peptide
LSLRNPILV
['C']

Species


Locus / Allele group


Publication

Epitope-specific TCRbeta repertoire diversity imparts no functional advantage on the CD8+ T cell response to cognate viral peptides.

La Gruta NL, Thomas PG, Webb AI, Dunstone MA, Cukalac T, Doherty PC, Purcell AW, Rossjohn J, Turner SJ
Proc. Natl. Acad. Sci. U.S.A. (2008) 105, 2034-9 [doi:10.1073/pnas.0711682102]  [pubmed:18238896

TCR repertoire diversity has been convincingly shown to facilitate responsiveness of CD8+ T cell populations to mutant virus peptides, thereby safeguarding against viral escape. However, the impact of repertoire diversity on the functionality of the CD8+ T cell response to cognate peptide-MHC class I complex (pMHC) recognition remains unclear. Here, we have compared TCRbeta chain repertoires of three influenza A epitope-specific CD8+ T cell responses in C57BL/6 (B6) mice: D(b)NP(366-374), D(b)PA(224-233), and a recently described epitope derived from the +1 reading frame of the influenza viral polymerase B subunit (residues 62-70) (D(b)PB1-F2(62)). Corresponding to the relative antigenicity of the respective pMHCs, and irrespective of the location of prominent residues, the D(b)PA(224)- and D(b)PB1-F2(62)-specific repertoires were similarly diverse, whereas the D(b)NP(366) population was substantially narrower. Importantly, parallel analysis of response magnitude, cytotoxicity, TCR avidity, and cytokine production for the three epitope-specific responses revealed no obvious functional advantage conferred by increased T cell repertoire diversity. Thus, whereas a diverse repertoire may be important for recognition of epitope variants, its effect on the response to cognate pMHC recognition appears minimal.

Structure deposition and release

Deposited: 2008-01-03
Released: 2008-03-25
Revised: 2011-07-13

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: LSLRNPILV

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

GLU163
TRP167
ARG62
TYR171
TYR159
TYR59
TYR7
PHE33
MET5
GLU63
LYS66
P2 SER

SER24
GLU63
LYS66
TYR45
TYR159
TYR7
P3 LEU

HIS155
TYR159
GLU9
LEU114
TYR156
LYS66
GLN97
GLN70
SER99
P4 ARG

ARG62
TYR156
LYS66
GLN70
HIS155
P5 ASN

TRP73
TYR156
GLN97
GLN70
PHE74
PHE116
P6 PRO

HIS155
TRP73
ALA152
TYR156
P7 ILE

TRP147
SER150
LYS146
TRP73
ALA152
TYR156
P8 LEU

ASN80
LYS146
GLN72
TRP73
VAL76
SER77
THR143
TRP147
P9 VAL

THR143
TYR123
LYS146
ASN80
TYR84
LEU81
ILE142
SER77
TRP73
TRP147

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

LEU159
CYS163
LEU167
LEU171
ARG5
TRP59
THR63
ALA66
PHE7
B Pocket

VAL24
ARG34
GLU45
THR63
ALA66
LYS67
PHE7
GLU70
THR9
GLY99
C Pocket

GLU70
PHE73
ARG74
THR9
MET97
D Pocket

GLN114
TYR155
LYS156
LEU159
GLU160
GLY99
E Pocket

GLN114
GLU147
ALA152
LYS156
MET97
F Pocket

ALA116
ILE123
ARG143
TRP146
GLU147
LEU77
LEU80
LEU81
TYR84
GLN95

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-Db
        10        20        30        40        50        60
PHSMRYFETAVSRPGLEEPRYISVGYVDNKEFVRFDSDAENPRYEPRAPWMEQEGPEYWE
        70        80        90       100       110       120
RETQKAKGQEQWFRVSLRNLLGYYNQSAGGSHTLQQMSGCDLGSDWRLLRGYLQFAYEGR
       130       140       150       160       170       180
DYIALNEDLKTWTAADMAAQITRRKWEQSGAAEHYKAYLEGECVEWLHRYLKNGNATLLR
       190       200       210       220       230       240
TDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGTF
       250       260       270
QKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRWEP

3. Peptide
LSLRNPILV


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. 3BUY assembly 1  

Components

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

Derived data

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

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