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6J2F

Ptal-N*01:01 binding "DYINTNVLP" at 1.90Å 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
DYINTNVLP
['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: Nonamer (9 amino acids)

Sequence: DYINTNVLP

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

ASN69
ARG65
TRP170
TYR102
ASN66
TYR7
TYR162
ASP59
TYR62
P2 TYR

GLY26
ALA45
TYR162
ALA24
ASN69
ARG35
PHE36
TYR102
VAL25
VAL34
ASN66
TYR7
ALA70
TYR9
P3 ILE

ARG100
ASP159
TYR102
ARG158
TYR162
TYR9
TYR155
ASN69
P4 ASN

ASP72
ASN69
P5 THR

ARG158
TYR155
ASP72
ARG100
P6 ASN

TYR9
TYR155
TYR77
ASP72
ASN69
THR76
ARG100
ALA73
P7 VAL

TYR155
THR76
TYR77
TRP150
ALA153
P8 LEU

TRP150
THR76
GLY80
GLN75
VAL79
ASN83
LYS149
P9 PRO

VAL84
ASN83
TYR126
ILE98
ASN145
GLY80
LYS149
TRP150
THR76
TYR77
TYR87
THR146

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
EPRTPKIQVYSRHPAENGKPNYLNCYVYGFHPPQIEIDLLKNGQKMKTEQSDLSFSKDWS
        70        80        90
FYLLVHTDFTPSTVDEYSCRVNHSSLAAPHMVKWDRNN

2. Class I alpha
Ptal-N*01:01
        10        20        30        40        50        60
GFHSLRYFYTAWSRPGSGEPRFVAVGYVDDTQFVRFDSDNASPRAEPRAPWMDLVEQQDP
        70        80        90       100       110       120
QYWDRNTRNARDAAQTYRVGLDNVRGYYNQSEAGSHTIQRMYGCDVGPHGRLLRGYDQLA
       130       140       150       160       170       180
YDGADYIALNEDLRSWTAADLAAQNTRRKWEEAGYAERDRAYLEGECVEWLLKHLENGRE
       190       200       210       220       230       240
TLLRADPPKTHITHHPISDREVTLRCWALGFYPEEITLTWQHDGEDQTQEMELVETRPDG
       250       260       270
NGAFQKWAALVVPSGEEQRYTCHVQHEGLPQPLTLRW

3. Peptide
DYINTNVLP


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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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. 6J2F assembly 1  
  2. 6J2F assembly 2  

Components

MHC Class I alpha chain [cif]
  1. 6J2F assembly 1  
  2. 6J2F assembly 2  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 6J2F assembly 1  
  2. 6J2F assembly 2  
Peptide only [cif]
  1. 6J2F assembly 1  
  2. 6J2F assembly 2  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/6j2f

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