5GSD

Crystal structure of LMP2 peptide from EBV in complex with HLA-A*11:01

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Dual non-contiguous peptide occupancy of HLA class I evoke antiviral human CD8 T cell response and form neo-epitopes with self-antigens

Xiao, Z., Ye, Z., Tadwal, V.S., Shen, M., Ren, E.C.

(2017) Sci Rep 7: 5072-5072

  • DOI: 10.1038/s41598-017-05171-w
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Host CD8 T cell response to viral infections involves recognition of 8-10-mer peptides presented by MHC-I molecules. However, proteasomes generate predominantly 2-7-mer peptides, but the role of these peptides is largely unknown. Here, we show that s ...

    Host CD8 T cell response to viral infections involves recognition of 8-10-mer peptides presented by MHC-I molecules. However, proteasomes generate predominantly 2-7-mer peptides, but the role of these peptides is largely unknown. Here, we show that single short peptides of <8-mer from Latent Membrane Protein 2 (LMP2) of Epstein Barr Virus (EBV) can bind HLA-A*11:01 and stimulate CD8+ cells. Surprisingly, two peptide fragments between 4-7-mer derived from LMP2(340-349) were able to complement each other, forming combination epitopes that can stimulate specific CD8+ T cell responses. Moreover, peptides from self-antigens can complement non-self peptides within the HLA binding cleft, forming neoepitopes. Solved structures of a tetra-complex comprising two peptides, HLA and β2-microglobulin revealed the free terminals of the two peptides to adopt an upward conformation directed towards the T cell receptor. Our results demonstrate a previously unknown mix-and-match combination of dual peptide occupancy in HLA that can generate vast combinatorial complexity.

    Organizational Affiliation: 

    Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, #03-06 Immunos, Singapore, 138648, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class I histocompatibility antigen, A-11 alpha chain
A
275Homo sapiensMutation(s): 0 
Gene Names: HLA-A (HLAA)
Find proteins for P13746 (Homo sapiens)
Go to Gene View: HLA-A
Go to UniProtKB:  P13746
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
99Homo 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
Epstein Barr Virus, Latent membrane protein-2 epitope
C
7Epstein-Barr virus (strain B95-8)Mutation(s): 0 
Gene Names: LMP2
Find proteins for P13285 (Epstein-Barr virus (strain B95-8))
Go to UniProtKB:  P13285
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download SDF File 
Download CCD File 
A, B
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: 2.3 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.353α = 90.00
b = 67.646β = 90.00
c = 115.603γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
SADABSdata reduction
SADABSdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-09
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Data collection