5FA4

Structure of HLA-A2:01 with peptide Y16R


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Unconventional Peptide Presentation by Major Histocompatibility Complex (MHC) Class I Allele HLA-A*02:01: BREAKING CONFINEMENT.

Remesh, S.G.Andreatta, M.Ying, G.Kaever, T.Nielsen, M.McMurtrey, C.Hildebrand, W.Peters, B.Zajonc, D.M.

(2017) J. Biol. Chem. 292: 5262-5270

  • DOI: 10.1074/jbc.M117.776542
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Peptide antigen presentation by major histocompatibility complex (MHC) class I proteins initiates CD8 <sup>+ </sup> T cell-mediated immunity against pathogens and cancers. MHC I molecules typically bind peptides with 9 amino acids in length with both ...

    Peptide antigen presentation by major histocompatibility complex (MHC) class I proteins initiates CD8 + T cell-mediated immunity against pathogens and cancers. MHC I molecules typically bind peptides with 9 amino acids in length with both ends tucked inside the major A and F binding pockets. It has been known for a while that longer peptides can also bind by either bulging out of the groove in the middle of the peptide or by binding in a zigzag fashion inside the groove. In a recent study, we identified an alternative binding conformation of naturally occurring peptides from Toxoplasma gondii bound by HLA-A*02:01. These peptides were extended at the C terminus (PΩ) and contained charged amino acids not more than 3 residues after the anchor amino acid at PΩ, which enabled them to open the F pocket and expose their C-terminal extension into the solvent. Here, we show that the mechanism of F pocket opening is dictated by the charge of the first charged amino acid found within the extension. Although positively charged amino acids result in the Tyr-84 swing, amino acids that are negatively charged induce a not previously described Lys-146 lift. Furthermore, we demonstrate that the peptides with alternative binding modes have properties that fit very poorly to the conventional MHC class I pathway and suggest they are presented via alternative means, potentially including cross-presentation via the MHC class II pathway.


    Organizational Affiliation

    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California 92037.,Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, CP1650 San Martín, Argentina.,Department of Microbiology and Immunology, University of Oklahoma Health Science Center, Oklahoma City, Oklahoma 73104.,Center for Biological Sequence Analysis, Department of Bio and Health Informatics, The Technical University of Denmark, 2800 Lyngby, Denmark.,From the Division for Cell Biology and.,From the Division for Cell Biology and dzajonc@lji.org.,Pure MHC LLC, Austin, Texas 78229, and.,Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class I histocompatibility antigen, A-2 alpha chain
A
274Homo sapiensMutation(s): 0 
Gene Names: HLA-A (HLAA)
Find proteins for P04439 (Homo sapiens)
Go to Gene View: HLA-A
Go to UniProtKB:  P04439
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
100Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Peptide Y16R
C
11N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 56.525α = 90.00
b = 79.421β = 116.42
c = 58.513γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2018-05-09
    Type: Data collection, Database references