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6AMU

HLA-A*02:01 presenting "MMWDRGLGMM" to Alpha/Beta T cell receptor at 2.15Å 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']
2. Class I alpha
HLA-A*02:01
['A']
3. Peptide
MMWDRGLGMM
['C']
4. T cell receptor alpha
TRAV12
['D']
5. T cell receptor beta
TRBV6
['E']

Species


Locus / Allele group


Publication

Crystal structure of DMF5 TCR bound to HLA-A2 presenting synthetic peptide MMWDRGLGMM

Riley, T.P., Baker, B.M.

Structure deposition and release

Deposited: 2017-08-11
Released: 2018-08-15
Revised: 2018-08-15

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication


Peptide details

Length: Decamer (10 amino acids)

Sequence: MMWDRGLGMM

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 MET

LYS66
TYR59
THR163
TRP167
PHE33
MET5
TYR7
TYR171
TYR159
GLU63
P10 MET

VAL76
LYS146
ASP77
THR80
VAL152
TRP147
ALA150
P2 MET

TYR7
HIS70
PHE9
MET45
VAL67
TYR159
TYR99
GLU63
LYS66
P3 TRP

TYR159
GLN155
LYS66
VAL152
HIS114
LEU156
ARG97
HIS70
TYR99
P4 ASP

LYS66
P5 ARG

VAL152
ALA150
HIS70
GLN155
P6 GLY

HIS70
P7 LEU

VAL152
TYR116
TRP147
ARG97
ASP77
THR73
HIS114
P8 GLY

TRP147
THR73
ASP77
THR143
TYR116
P9 MET

TRP147
THR143
TYR123
TYR116
LEU81
LYS146
ASP77
THR80
TYR84
VAL95

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
VAL66
PHE7
B Pocket

VAL24
ARG34
GLU45
THR63
VAL66
LYS67
PHE7
SER70
THR9
GLY99
C Pocket

SER70
HIS73
ARG74
THR9
MET97
D Pocket

GLN114
LEU155
ARG156
LEU159
GLU160
GLY99
E Pocket

GLN114
GLU147
ALA152
ARG156
MET97
F Pocket

ALA116
ILE123
LYS143
TRP146
GLU147
LEU77
LEU80
ARG81
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
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
SHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWD
        70        80        90       100       110       120
GETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGK
       130       140       150       160       170       180
DYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQR
       190       200       210       220       230       240
TDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTF
       250       260       270
QKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRW

3. Peptide
MMWDRGLGMM

4. T cell receptor alpha
T cell receptor alpha
TRAV12
        10        20        30        40        50        60
EVEQNSGPLSVPEGAIASLNCTYSDRGSQSFFWYRQYSGKSPELIMFIYSNGDKEDGRFT
        70        80        90       100       110       120
AQLNKASQYVSLLIRDSQPSDSATYLCAVNFGGGKLIFGQGTELSVKPNIQNPDPAVYQL
       130       140       150       160       170       180
RDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFA
       190
CANAFNNSIIPEDTFFP

5. T cell receptor beta
T cell receptor beta
TRBV6
        10        20        30        40        50        60
IAGITQAPTSQILAAGRRMTLRCTQDMRHNAMYWYRQDLGLGLRLIHYSNTAGTTGKGEV
        70        80        90       100       110       120
PDGYSVSRANTDDFPLTLASAVPSQTSVYFCASSLSFGTEAFFGQGTRLTVVEDLNKVFP
       130       140       150       160       170       180
PEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPA
       190       200       210       220       230       240
LNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR

A


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. 6AMU assembly 1  

Components

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

Derived data

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

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