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6LB2

Mamu-B*098:08 possibly without "peptide" at 1.69Å 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 possibly without peptide

1. Beta 2 microglobulin
['B', 'D']
2. Class I alpha
Mamu-B*098:08
['A', 'C']

Species


Locus / Allele group


Publication

Crystal structures of lysophospholipid-bound MHC class I molecules.

Shima Y, Morita D, Mizutani T, Mori N, Mikami B, Sugita M
J. Biol. Chem. (2020) [doi:10.1074/jbc.RA119.011932]  [pubmed:32269076

Newly synthesized major histocompatibility complex (MHC) class I proteins are stabilized in the endoplasmic reticulum (ER) by binding 8-10-mer-long self-peptide antigens that are provided by transporter associated with antigen processing (TAP). These MHC class I:peptide complexes then exit the ER and reach the plasma membrane, serving to sustain the steady-state MHC class I expression on the cell surface. A novel subset of MHC class I molecules that preferentially bind lipid-containing ligands rather than conventional peptides was recently identified. The primate classical MHC class I allomorphs, Mamu-B*098 and Mamu-B*05104, are capable of binding the N-myristoylated 5-mer (C14-Gly-Gly-Ala-Ile-Ser) or 4-mer (C14-Gly-Gly-Ala-Ile) lipopeptides derived from the N-myristoylated SIV Nef protein, respectively, and of activating lipopeptide antigen-specific cytotoxic T lymphocytes. We herein demonstrate that Mamu-B*098 samples lysophosphatidylethanolamine and lysophosphatidylcholine containing up to a C20 fatty acid in the ER. The X-ray crystal structures of Mamu-B*098 and Mamu-B*05104 complexed with lysophospholipids at high resolution revealed that the B and D pockets in the antigen-binding grooves of these MHC class I molecules accommodate these lipids through a monoacylglycerol moiety. Consistent with the capacity to bind cellular lipid ligands, these two MHC class I molecules did not require TAP function for cell-surface expression. Collectively, these results indicate that peptide- and lipopeptide-presenting MHC class I subsets use distinct sources of endogenous ligands.

Structure deposition and release

Deposited: 2019-11-13
Released: 2020-04-22
Revised: 2020-05-27

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication


Binding cleft pockets


Peptide sidechain binding pockets (static)
Peptide terminii and backbone binding residues (static)
A Pocket

ALA159
GLY163
GLU167
ARG171
SER5
GLU59
GLU63
ARG66
ARG7
B Pocket

ILE24
PHE34
LYS45
GLU63
ARG66
ARG67
ARG7
ASP70
PHE9
MET99
C Pocket

ASP70
GLN73
THR74
PHE9
GLN97
D Pocket

TYR114
GLU155
GLN156
ALA159
TYR160
MET99
E Pocket

TYR114
LYS147
GLY152
GLN156
GLN97
F Pocket

GLN116
ASP123
ASN143
ARG146
LYS147
VAL77
GLY80
ASN81
GLY84
THR95

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
AIQRTPKIQVYSRHPPENGKPNFLNCYVSGFHPSDIEVDLLKNGEKMGKVEHSDLSFSKD
        70        80        90
WSFYLLYYTEFTPNEKDEYACRVNHVTLSGPRTVKWDRDM

2. Class I alpha
Mamu-B*098:08
        10        20        30        40        50        60
AGSHSMRYFSTTVSRPGRGEPRFIVVGYVDDTQFVRFDSDAASPKMEPRAPWMEQEGPEY
        70        80        90       100       110       120
WEEQTRRVKDAAQTFRVSLGNLRGYYNQSEAGSHTLQTMSGCDLGPDGRLLRGYYQQAYD
       130       140       150       160       170       180
GRDYIALNEDLRSWTAADEAAQNTQRKWEAAGVAEQWRAYLEGECLESLRRYLENGKETL
       190       200       210       220       230       240
QRAEPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPGGDG
       250       260       270
TFQKWGAVVVPSGEEQRYTCHVQHEGLPEPLTLRWEP


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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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. 6LB2 assembly 1  
  2. 6LB2 assembly 2  

Components

MHC Class I alpha chain [cif]
  1. 6LB2 assembly 1  
  2. 6LB2 assembly 2  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 6LB2 assembly 1  
  2. 6LB2 assembly 2  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/6lb2

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