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7JYX

HLA-A*24:02 binding "TYQWIIRNWET" at 2.95Å 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', 'E']
2. Class I alpha
HLA-A*24:02
['A', 'D']
3. Peptide
TYQWIIRNWET
['C', 'F']

Species


Locus / Allele group


Publication

CD8+ T cell landscape in Indigenous and non-Indigenous people restricted by influenza mortality-associated HLA-A*24:02 allomorph.

Hensen L, Illing PT, Bridie Clemens E, Nguyen THO, Koutsakos M, van de Sandt CE, Mifsud NA, Nguyen AT, Szeto C, Chua BY, Halim H, Rizzetto S, Luciani F, Loh L, Grant EJ, Saunders PM, Brooks AG, Rockman S, Kotsimbos TC, Cheng AC, Richards M, Westall GP, Wakim LM, Loudovaris T, Mannering SI, Elliott M, Tangye SG, Jackson DC, Flanagan KL, Rossjohn J, Gras S, Davies J, Miller A, Tong SYC, Purcell AW, Kedzierska K
Nat Commun (2021) 12, 2931 [doi:10.1038/s41467-021-23212-x]  [pubmed:34006841

Background

The majority of clinical genetic testing focuses almost exclusively on regions of the genome that directly encode proteins. The important role of variants in non-coding regions in penetrant disease is, however, increasingly being demonstrated, and the use of whole genome sequencing in clinical diagnostic settings is rising across a large range of genetic disorders. Despite this, there is no existing guidance on how current guidelines designed primarily for variants in protein-coding regions should be adapted for variants identified in other genomic contexts.

Methods

We convened a panel of nine clinical and research scientists with wide-ranging expertise in clinical variant interpretation, with specific experience in variants within non-coding regions. This panel discussed and refined an initial draft of the guidelines which were then extensively tested and reviewed by external groups.

Results

We discuss considerations specifically for variants in non-coding regions of the genome. We outline how to define candidate regulatory elements, highlight examples of mechanisms through which non-coding region variants can lead to penetrant monogenic disease, and outline how existing guidelines can be adapted for the interpretation of these variants.

Conclusions

These recommendations aim to increase the number and range of non-coding region variants that can be clinically interpreted, which, together with a compatible phenotype, can lead to new diagnoses and catalyse the discovery of novel disease mechanisms.

Structure deposition and release

Deposited: 2020-09-01
Released: 2021-04-14
Revised: 2021-06-23

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication


Peptide details

Length: Undecamer (11 amino acids)

Sequence: TYQWIIRNWET

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 THR

GLU63
TYR7
PHE99
MET5
GLY167
PHE33
TYR171
THR163
CYS164
TYR159
TYR59
LYS66
P10 GLU

THR143
ARG83
LYS146
TYR84
ILE80
P11 THR

TRP147
LYS146
P2 TYR

TYR159
LYS66
TYR7
HIS70
GLU63
MET45
ALA24
PHE22
VAL67
SER9
PHE99
P3 GLN

GLN155
PHE99
GLN156
LEU160
TYR159
LYS66
HIS114
P4 TRP

LYS66
GLY65
GLN156
GLN155
ALA69
P5 ILE

PHE99
ASP74
ALA69
THR73
TYR116
HIS70
HIS114
MET97
P6 ILE

GLN155
ALA69
THR73
P7 ARG

ALA150
VAL152
ASN77
LYS146
GLN155
THR73
TRP147
P8 ASN

ASN77
GLU76
THR73
TRP147
ILE80
P9 TRP

TRP147
ILE124
ILE80
TYR116
ASN77
THR143
TYR118
ILE142
TYR123
LYS146
TYR84
LEU95
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
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEPSS

3. Peptide
TYQWIIRNWET


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.
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   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]
  1. 7JYX assembly 1  
  2. 7JYX assembly 2  

Components

MHC Class I alpha chain [cif]
  1. 7JYX assembly 1  
  2. 7JYX assembly 2  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 7JYX assembly 1  
  2. 7JYX assembly 2  
Peptide only [cif]
  1. 7JYX assembly 1  
  2. 7JYX assembly 2  

Derived data

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

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