6A6H

Crystal Structure of Swine Major Histocompatibility Complex Class I SLA-2*040202 For 2.3 Angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.203 

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This is version 1.2 of the entry. See complete history


Literature

Crystallization of SLA-2*04:02:02 complexed with a CTL epitope derived from FMDV.

Ning, S.Wang, Z.B.Qi, P.Xiao, J.Wang, X.J.

(2019) Res Vet Sci 128: 90-98

  • DOI: 10.1016/j.rvsc.2019.11.002
  • Primary Citation of Related Structures:  
    6A6H

  • PubMed Abstract: 
  • Presentation of viral epitopes by swine MHC I (termed leukocyte antigen class I, SLA I) to cytotoxic T lymphocytes (CTLs) is crucial for swine immunity. The SLA-2 structure, however, remains largely unknown. To illustrate the structural basis of swin ...

    Presentation of viral epitopes by swine MHC I (termed leukocyte antigen class I, SLA I) to cytotoxic T lymphocytes (CTLs) is crucial for swine immunity. The SLA-2 structure, however, remains largely unknown. To illustrate the structural basis of swine CTL epitope presentation, the crystal structure of SLA-2*04:02:02 complexed with one peptide, derived from foot-and-mouth disease virus (FMDV), was analyzed in this study. SLA-2*04:02:02 and swine β2-microglobulin (sβ2m) were refolded in vitro in the presence of peptides. X-ray diffraction data of SLA-2*04:02:02-peptide-sβ2m (referred to as p/SLA-2*04:02:02) were collected. The diffraction dataset was 2.3 Å in resolution and the space group was P3(2)21. Relevant data included a = 101.8 Å, b = 101.8 Å, c = 73.455 Å,α = 90.00°, β = 90.00°, γ = 120.00°. The structure of p/SLA-2*04:02:02 was analyzed. The results revealed that Glu24, Met68, Gly76, and Gln173 in PBG of SLA-2*04:02:02 are different from other MHC I. Furthermore, Asn63 is different from other SLA I. Gln57, Met174 and Gln180 in PBG of SLA I are different from other species' MHC I. All of these features are different from known mammalian peptide-MHC class I complexes (referred to as p/MHC I). In addition, P4-His, P6-Val, and P8-Pro in the peptide were exposed, and these residues as epitopes can be presented by SLA-2*04:02:02. This study not only provides a structural basis for peptide presentation by SLA-2, but also screens one potential FMDV CTL epitope. The results may be of interest in future vaccine development.


    Organizational Affiliation

    Key Laboratory of Epidemiology of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, China. Electronic address: wangxj@cau.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MHC class I antigenA275Sus scrofaMutation(s): 0 
Gene Names: SLA-BSLA-2
Find proteins for Q8MHU4 (Sus scrofa)
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Go to UniProtKB:  Q8MHU4
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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
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
MET-THR-ALA-HIS-ILE-VAL-VAL-PRO-TYRC9Foot-and-mouth disease virus - type AMutation(s): 0 
EC: 3.4.22.46 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P49303 (Foot-and-mouth disease virus (isolate -/Azerbaijan/A22-550/1965 serotype A))
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Go to UniProtKB:  P49303
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.203 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.802α = 90
b = 101.802β = 90
c = 73.455γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2018-06-28 
  • Released Date: 2019-07-03 
  • Deposition Author(s): Ning, S., Wang, Z.B.

Revision History 

  • Version 1.0: 2019-07-03
    Type: Initial release
  • Version 1.1: 2019-10-30
    Changes: Data collection
  • Version 1.2: 2020-01-15
    Changes: Database references