5YLX

Integrated illustration of a valid epitope based on the SLA class I structure and tetramer technique could carry forward the development of molecular vaccine in swine species


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Illumination of PRRSV Cytotoxic T Lymphocyte Epitopes by the Three-Dimensional Structure and Peptidome of Swine Lymphocyte Antigen Class I (SLA-I).

Pan, X.Zhang, N.Wei, X.Jiang, Y.Chen, R.Li, Q.Liang, R.Zhang, L.Ma, L.Xia, C.

(2019) Front Immunol 10: 2995-2995

  • DOI: 10.3389/fimmu.2019.02995
  • Primary Citation of Related Structures:  
    5YLX

  • PubMed Abstract: 
  • To investigate CTL epitope applications in swine, SLA-1 * 1502-restricted peptide epitopes matching porcine reproductive and respiratory syndrome virus (PRRSV) strains were explored by crystallography, biochemistry, and the specific pathog ...

    To investigate CTL epitope applications in swine, SLA-1 * 1502-restricted peptide epitopes matching porcine reproductive and respiratory syndrome virus (PRRSV) strains were explored by crystallography, biochemistry, and the specific pathogen-free (SPF) swine experiments. First, nine predicted PRRSV peptides were tested by assembly of the peptide-SLA-1 * 1502 (pSLA-1 * 1502) complexes, and the crystal structure of the SLA-1 * 1502 complex with one peptide (NSP9-TMP9) was determined. The NSP9-TMP9 peptide conformation presented by pSLA-1 * 1502 is different from that of the peptides presented by the known pSLA-1 * 0401 and pSLA-3 * hs0202 complexes. Two consecutive Pro residues make the turn between P3 and P4 of NSP9-TMP9 much sharper. The D pocket of pSLA-1 * 1502 is unique and is important for peptide binding. Next, the potential SLA-1 * 1502-restricted peptide epitopes matching four typical genetic PRRSV strains were identified based on the peptide-binding motif of SLA-1 * 1502 determined by structural analysis and alanine scanning of the NSP9-TMP9 peptide. The tetrameric complex of SLA-1 * 1502 and NSP9-TMP9 was constructed and examined. Finally, taking NSP9-TMP9 as an example, the CTL immunogenicity of the identified PRRSV peptide epitope was evaluated. The SPF swine expressing the SLA-1 * 1502 alleles were divided into three groups: modified live vaccine (MLV), MLV+NSP9-TMP9, and the blank control group. NSP9-TMP9 was determined as a PRRSV CTL epitope with strong immunogenicity by flow cytometry and IFN-γ expression. Our study developed an integrated approach to identify SLA-I-restricted CTL epitopes from various important viruses and is helpful in designing and applying effective peptide-based vaccines for swine.


    Organizational Affiliation

    Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, China Agricultural University, Beijing, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MHC class I antigenA275Sus scrofaMutation(s): 0 
Gene Names: SLA-1
Find proteins for H6TIB1 (Sus scrofa)
Explore H6TIB1 
Go to UniProtKB:  H6TIB1
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB98Sus scrofaMutation(s): 0 
Gene Names: B2M
Find proteins for Q07717 (Sus scrofa)
Explore Q07717 
Go to UniProtKB:  Q07717
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PRRSV-NSP9-TMP9 peptideC9Porcine reproductive and respiratory syndrome virusMutation(s): 0 
EC: 3.4.22 (UniProt), 3.4.19.12 (UniProt), 3.4.21 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt)
Find proteins for Q9YN02 (Porcine reproductive and respiratory syndrome virus (strain 16244B))
Explore Q9YN02 
Go to UniProtKB:  Q9YN02
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.058α = 90
b = 74.059β = 90
c = 98.596γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31201887
863 Project of the China Ministry of Science and TechnologyChina2013AA102503
973 Project of the China Ministry of Science and TechnologyChina2013CB835302

Revision History 

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2018-11-07
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2020-05-06
    Changes: Database references