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7NMF

HLA-A*24:02 presenting "QLPRLFPLL" to Alpha/Beta T cell receptor at 2.98Å 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*24:02
['A']
3. Peptide
QLPRLFPLL
['C']
4. T cell receptor alpha
TRAV5
['D']
5. T cell receptor beta
TRBV7
['E']

Species


Locus / Allele group


Publication

Human MHC Class I, A24 Allele presenting QLPRLFPLL, Complex with 4C6 TCR, monoclinic form

Rizkallahp, P.J., Sewell, A.K., Cole, D.K., Wall, A.

Structure deposition and release

Deposited: 2021-02-23
Released: 2022-09-07
Revised: 2022-09-07

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: QLPRLFPLL

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 GLN

GLU63
PHE33
ASP166
ARG170
TYR171
TYR159
TYR59
TYR7
LYS66
CYS164
GLU62
THR163
GLY167
MET5
P2 LEU

TYR159
TYR7
LYS66
HIS70
THR163
MET45
PHE99
GLU63
VAL67
P3 PRO

TYR159
LYS66
GLN156
PHE99
P4 ARG

LYS66
P5 LEU

GLN155
GLN156
P6 PHE

HIS70
HIS114
PHE99
GLN156
MET97
TYR116
THR73
LYS66
P7 PRO

ASN77
TRP147
HIS114
VAL152
GLN156
ASP74
TYR116
THR73
P8 LEU

THR143
THR73
ASN77
ILE80
TRP147
P9 LEU

ASN77
ILE124
THR143
TYR84
LEU95
TYR123
LYS146
TYR116
ILE80
TRP147
ALA81

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
GLY167
TYR171
MET5
TYR59
GLU63
LYS66
TYR7
B Pocket

ALA24
VAL34
MET45
GLU63
LYS66
VAL67
TYR7
HIS70
SER9
PHE99
C Pocket

HIS70
THR73
ASP74
SER9
MET97
D Pocket

HIS114
GLN155
GLN156
TYR159
LEU160
PHE99
E Pocket

HIS114
TRP147
VAL152
GLN156
MET97
F Pocket

TYR116
TYR123
THR143
LYS146
TRP147
ASN77
ILE80
ALA81
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
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
        70        80        90
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

2. Class I alpha
HLA-A*24:02
IPD-IMGT/HLA
[ipd-imgt:HLA34790]
        10        20        30        40        50        60
GSHSMRYFSTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
        70        80        90       100       110       120
DEETGKVKAHSQTDRENLRIALRYYNQSEAGSHTLQMMFGCDVGSDGRFLRGYHQYAYDG
       130       140       150       160       170       180
KDYIALKEDLRSWTAADMAAQITKRKWEAAHVAEQQRAYLEGTCVDGLRRYLENGKETLQ
       190       200       210       220       230       240
RTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
       250       260       270
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

3. Peptide
QLPRLFPLL

4. T cell receptor alpha
T cell receptor alpha
TRAV5
        10        20        30        40        50        60
GEDVEQSLFLSVREGDSSVINCTYTDSSSTYLYWYKQEPGAGLQLLTYIFSNMDMKQDQR
        70        80        90       100       110       120
LTVLLNKKDKHLSLRIADTQTGDSAIYFCAEPSGNTGKLIFGQGTTLQVKPIQNPDPAVY
       130       140       150       160       170       180
QLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSD
       190
FACANAFNNSIIPE

5. T cell receptor beta
T cell receptor beta
TRBV7
        10        20        30        40        50        60
TGVSQDPRHKITKRGQNVTFRCDPISEHNRLYWYRQTLGQGPEFLTYFQNEAQLEKSRLL
        70        80        90       100       110       120
SDRFSAERPKGSFSTLEIQRTEQGDSAMYLCASSLHHEQYFGPGTRLTVTEDLKNVFPPE
       130       140       150       160       170       180
VAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALN
       190       200       210       220       230
DSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD


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. 7NMF assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 7NMF assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 7NMF assembly 1  
Peptide only [cif]
  1. 7NMF assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/7nmf

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