5D9S

Structure of HLA-A2:01 with the 11-mer peptide F11V

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


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


Literature

Toxoplasma gondii peptide ligands open the gate of the HLA class I binding groove.

McMurtrey, C., Trolle, T., Sansom, T., Remesh, S.G., Kaever, T., Bardet, W., Jackson, K., McLeod, R., Sette, A., Nielsen, M., Zajonc, D.M., Blader, I.J., Peters, B., Hildebrand, W.

(2016) Elife 5

  • DOI: 10.7554/eLife.12556
  • Primary Citation of Related Structures:  
    5D9S, 5DDH

  • PubMed Abstract: 

    • HLA class I presentation of pathogen-derived peptide ligands is essential for CD8+ T-cell recognition of Toxoplasma gondii infected cells. Currently, little data exist pertaining to peptides that are presented after T. gondii infection. Herein we pur ...

    HLA class I presentation of pathogen-derived peptide ligands is essential for CD8+ T-cell recognition of Toxoplasma gondii infected cells. Currently, little data exist pertaining to peptides that are presented after T. gondii infection. Herein we purify HLA-A*02:01 complexes from T. gondii infected cells and characterize the peptide ligands using LCMS. We identify 195 T. gondii encoded ligands originating from both secreted and cytoplasmic proteins. Surprisingly, T. gondii ligands are significantly longer than uninfected host ligands, and these longer pathogen-derived peptides maintain a canonical N-terminal binding core yet exhibit a C-terminal extension of 1-30 amino acids. Structural analysis demonstrates that binding of extended peptides opens the HLA class I F' pocket, allowing the C-terminal extension to protrude through one end of the binding groove. In summary, we demonstrate that unrealized structural flexibility makes MHC class I receptive to parasite-derived ligands that exhibit unique C-terminal peptide extensions.

    Organizational Affiliation: 

    Pure MHC LLC, Austin, United States.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-2 alpha chainA274Homo sapiensMutation(s): 0 
Gene Names: HLA-A, HLAA
Find proteins for P04439 (Homo sapiens)
Explore P04439 
Go to UniProtKB:  P04439
NIH Common Fund Data Resources
PHAROS  P04439
GTEx  ENSG00000206503
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB100Homo sapiensMutation(s): 0 
Gene Names: B2M, CDABP0092, HDCMA22P
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769
GTEx  ENSG00000166710
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
11-mer peptide F11VC11Toxoplasma gondiiMutation(s): 0 
Find proteins for S7UWA0 (Toxoplasma gondii (strain ATCC 50853 / GT1))
Explore S7UWA0 
Go to UniProtKB:  S7UWA0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.33α = 90
b = 80.238β = 113.17
c = 56.855γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
Cootmodel building
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-06
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Derived calculations, Refinement description