1MI5

HLA-B*08:01 presenting "FLRGRAYGL" 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.

Complex type

Class i with peptide and alpha beta tcr

1. Beta 2 microglobulin

['B']

2. Class I alpha
HLA-B*08:01

['A']

3. Peptide
FLRGRAYGL

['C']

4. T cell receptor alpha
TRAV26

['D']

5. T cell receptor beta
TRBV7

['E']

Information on this structure on STCRdab.

Species

Homo sapiens (Human)

Locus / Allele group

HLA-B / HLA-B*08

Publication

A structural basis for the selection of dominant alphabeta T cell receptors in antiviral immunity.

Kjer-Nielsen L, Clements CS, Purcell AW, Brooks AG, Whisstock JC, Burrows SR, McCluskey J, Rossjohn J

Immunity (2003) 18, 53-64 [doi:10.1016/s1074-7613(02)00513-7] [pubmed:12530975]

We have examined the basis for immunodominant or "public" TCR usage in an antiviral CTL response. Residues encoded by each of the highly selected genetic elements of an immunodominant clonotype recognizing Epstein-Barr virus were critical to the antigen specificity of the receptor. Upon recognizing antigen, the immunodominant TCR undergoes extensive conformational changes in the complementarity determining regions (CDRs), including the disruption of the canonical structures of the germline-encoded CDR1alpha and CDR2alpha loops to produce an enhanced fit with the HLA-peptide complex. TCR ligation induces conformational changes in the TCRalpha constant domain thought to form part of the docking site for CD3epsilon. These findings indicate that TCR immunodominance is associated with structural properties conferring receptor specificity and suggest a novel structural link between TCR ligation and intracellular signaling.

Structure deposition and release

Deposited: 2002-08-21

Released: 2003-02-04

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: FLRGRAYGL

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 PHE

ARG62

TYR159

TYR7

THR163

ASN63

ILE66

MET5

TYR59

TRP167

PHE33

TYR171

P2 LEU

PHE67

TYR159

SER24

TYR7

ILE66

ASP9

TYR99

ASN63

ASN70

PHE36

P3 ARG

ILE66

ASN114

ASP156

TYR99

VAL152

ASN70

GLN155

TYR159

TYR116

P4 GLY

GLN155

ASN70

ILE66

P5 ARG

ASP9

TYR99

ASN70

THR73

ASP74

GLN155

THR69

TYR116

P6 ALA

GLU76

GLN155

THR73

P7 TYR

THR73

GLU76

ALA150

SER77

TRP147

VAL152

GLN155

P8 GLY

SER77

TRP147

ASN80

LYS146

THR73

GLU76

P9 LEU

LYS146

GLU76

THR143

TYR116

LEU81

SER77

TRP147

ASN80

ILE124

TYR84

TYR123

LEU95

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

ASN63

ILE66

TYR7

B Pocket

SER24

VAL34

GLU45

ASN63

ILE66

PHE67

TYR7

ASN70

ASP9

TYR99

C Pocket

ASN70

THR73

ASP74

ASP9

SER97

D Pocket

ASN114

GLN155

ASP156

TYR159

LEU160

TYR99

E Pocket

ASN114

TRP147

VAL152

ASP156

SER97

F Pocket

TYR116

TYR123

THR143

LYS146

TRP147

SER77

ASN80

LEU81

TYR84

LEU95

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 IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW 70 80 90 SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

2. Class I alpha HLA-B08:01 IPD-IMGT/HLA* [ipd-imgt:HLA34671]	10 20 30 40 50 60 GSHSMRYFDTAMSRPGRGEPRFISVGYVDDTQFVRFDSDAASPREEPRAPWIEQEGPEYW 70 80 90 100 110 120 DRNTQIFKTNTQTDRESLRNLRGYYNQSEAGSHTLQSMYGCDVGPDGRLLRGHNQYAYDG 130 140 150 160 170 180 KDYIALNEDLRSWTAADTAAQITQRKWEAARVAEQDRAYLEGTCVEWLRRYLENGKDTLE 190 200 210 220 230 240 RADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT 250 260 270 FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEPS

3. Peptide	FLRGRAYGL

4. T cell receptor alpha T cell receptor alpha TRAV26	10 20 30 40 50 60 KTTQPNSMESNEEEPVHLPCNHSTISGTDYIHWYRQLPSQGPEYVIHGLTSNVNNRMASL 70 80 90 100 110 120 AIAEDRKSSTLILHRATLRDAAVYYCILPLAGGTSYGKLTFGQGTILTVHPNIQNPDPAV 130 140 150 160 170 180 YQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTVLDMRSMDFKSNSAVAWSNKS 190 200 DFACANAFNNSIIPEDTFFPS

5. T cell receptor beta T cell receptor beta TRBV7	10 20 30 40 50 60 GVSQSPRYKVAKRGQDVALRCDPISGHVSLFWYQQALGQGPEFLTYFQNEAQLDKSGLPS 70 80 90 100 110 120 DRFFAERPEGSVSTLKIQRTQQEDSAVYLCASSLGQAYEQYFGPGTRLTVTEDLKNVFPP 130 140 150 160 170 180 EVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVSTDPQPLKEQPAL 190 200 210 220 230 240 NDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA D

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

Data can be downloaded to your local machine from the links below.

Clicking on the clipboard icon will copy the url for the data to your clipboard.

This can then be used to load the structure/data directly from the url into an application like PyMol (for 3D structures) using the load command:

e.g. load http://www.histo.fyi/structures/downloads/1hhk_1_peptide.cif

or in the case of JSON formatted files to retrieve it and use it as part of notebooks such as Jupyter or GoogleColab.

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]

1MI5 assembly 1

Components

MHC Class I alpha chain [cif]

1MI5 assembly 1

MHC Class I antigen binding domain (alpha1/alpha2) [cif]

1MI5 assembly 1

Peptide only [cif]

1MI5 assembly 1

Derived data

Data for this page [json]

https://api.histo.fyi/v1/structures/1mi5

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

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

This work is licensed under a Creative Commons Attribution 4.0 International License.