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6J2H

Ptal-N*01:01 binding "DFANTFLP" at 2.30Å 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
Ptal-N*01:01
['A', 'D']
3. Peptide
DFANTFLP
['C', 'F']

Species


Locus / Allele group


Publication

Peptide presentation by bat MHC class I provides new insight into the antiviral immunity of bats.

Lu D, Liu K, Zhang D, Yue C, Lu Q, Cheng H, Wang L, Chai Y, Qi J, Wang LF, Gao GF, Liu WJ
PLoS Biol. (2019) 17, e3000436 [doi:10.1371/journal.pbio.3000436]  [pubmed:31498797

Bats harbor many zoonotic viruses, including highly pathogenic viruses of humans and other mammals, but they are typically asymptomatic in bats. To further understand the antiviral immunity of bats, we screened and identified a series of bat major histocompatibility complex (MHC) I Ptal-N*01:01-binding peptides derived from four different bat-borne viruses, i.e., Hendra virus (HeV), Ebola virus (EBOV), Middle East respiratory syndrome coronavirus (MERS-CoV), and H17N10 influenza-like virus. The structures of Ptal-N*01:01 display unusual peptide presentation features in that the bat-specific 3-amino acid (aa) insertion enables the tight "surface anchoring" of the P1-Asp in pocket A of bat MHC I. As the classical primary anchoring positions, the B and F pockets of Ptal-N*01:01 also show unconventional conformations, which contribute to unusual peptide motifs and distinct peptide presentation. Notably, the features of bat MHC I may be shared by MHC I from various marsupials. Our study sheds light on bat adaptive immunity and may benefit future vaccine development against bat-borne viruses of high impact on humans.

Structure deposition and release

Deposited: 2019-01-01
Released: 2019-09-18
Revised: 2019-12-04

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication


Peptide details

Length: Octamer (8 amino acids)

Sequence: DFANTFLP

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 ASP

TYR159
TYR59
TYR7
GLU163
TYR99
ASN63
TRP167
ARG62
P2 PHE

ASN63
ALA45
ALA24
ALA67
PHE36
VAL34
TYR159
TYR7
ASN66
TYR99
TYR9
P3 ALA

TYR9
TYR99
ARG97
TYR159
ASN66
P4 ASN

ARG155
ARG97
ASN66
ASP156
P5 THR

TYR74
THR73
ARG97
ALA70
ASN66
TYR9
P6 PHE

ARG155
ARG97
ASP114
TYR74
TRP133
THR73
TRP147
ASP156
TYR152
P7 LEU

GLY77
TYR152
THR73
VAL76
TRP147
ASN80
THR143
P8 PRO

ILE95
TYR74
THR73
TYR123
TRP147
ASN80
THR143
TYR84
GLY77
LYS146
LEU116
VAL81

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]


Chain sequences

1. Beta 2 microglobulin
Beta 2 microglobulin
        10        20        30        40        50        60
SHIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSK
        70        80        90       100
DWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

2. Class I alpha
Ptal-N*01:01
        10        20        30        40        50        60
GFHSLRYFYTAWSRPGSGEPRFVAVGYVDDTQFVRFDSDNASPRAEPRAPWVEQQDPQYW
        70        80        90       100       110       120
DRNTRNARDAAQTYRVGLDNVRGYYNQSEAGSHTIQRMYGCDVGPHGRLLRGYDQLAYDG
       130       140       150       160       170       180
ADYIALNEDLRSWTAADLAAQNTRRKWEEAGYAERDRAYLEGECVEWLLKHLENGRETLL
       190       200       210       220       230       240
RADPPKTHITHHPISDREVTLRCWALGFYPEEITLTWQHDGEDQTQEMELVETRPDGNGA
       250       260       270
FQKWAALVVPSGEEQRYTCHVQHEGLPQPLTLRW

3. Peptide
DFANTFLP


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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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. 6J2H assembly 1  
  2. 6J2H assembly 2  

Components

MHC Class I alpha chain [cif]
  1. 6J2H assembly 1  
  2. 6J2H assembly 2  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 6J2H assembly 1  
  2. 6J2H assembly 2  
Peptide only [cif]
  1. 6J2H assembly 1  
  2. 6J2H assembly 2  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/6j2h

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