7ST3

Consequences of HLA single chain trimer mutations on peptide presentation and binding affinity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Effects of HLA single chain trimer design on peptide presentation and stability.

Finton, K.A.K.Rupert, P.B.Friend, D.J.Dinca, A.Lovelace, E.S.Buerger, M.Rusnac, D.V.Foote-McNabb, U.Chour, W.Heath, J.R.Campbell, J.S.Pierce, R.H.Strong, R.K.

(2023) Front Immunol 14: 1170462-1170462

  • DOI: https://doi.org/10.3389/fimmu.2023.1170462

  • PubMed Abstract: 

    MHC class I " single-chain trimer " molecules, coupling MHC heavy chain, β 2 -microglobulin, and a specific peptide into a single polypeptide chain, are widely used in research. To more fully understand caveats associated with this design that may affect its use for basic and translational studies, we evaluated a set of engineered single-chain trimers with combinations of stabilizing mutations across eight different classical and non-classical human class I alleles with 44 different peptides, including a novel human/murine chimeric design. While, overall, single-chain trimers accurately recapitulate native molecules, care was needed in selecting designs for studying peptides longer or shorter than 9-mers, as single-chain trimer design could affect peptide conformation. In the process, we observed that predictions of peptide binding were often discordant with experiment and that yields and stabilities varied widely with construct design. We also developed novel reagents to improve the crystallizability of these proteins and confirmed novel modes of peptide presentation.


  • Organizational Affiliation

    Division of Basic Science, Fred Hutchinson Cancer Research Center (FHCC), Seattle, WA, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera429Human papillomavirus 16Pongo pygmaeusHomo sapiens
This entity is chimeric
Mutation(s): 2 
Gene Names: E7B2MHLA-A
UniProt
Find proteins for P16213 (Pongo pygmaeus)
Explore P16213 
Go to UniProtKB:  P16213
Find proteins for P03129 (Human papillomavirus type 16)
Explore P03129 
Go to UniProtKB:  P03129
Find proteins for A0A678ZGP6 (Homo sapiens)
Explore A0A678ZGP6 
Go to UniProtKB:  A0A678ZGP6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP16213A0A678ZGP6P03129
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
VHH116Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.796α = 102.449
b = 118.041β = 102.452
c = 273.507γ = 89.998
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-23
    Type: Initial release
  • Version 1.1: 2023-05-31
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description