5H94

Crystal structure of Swine MHC CLASSI for 1.48 angstroms


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural and Biochemical Analyses of Swine Major Histocompatibility Complex Class I Complexes and Prediction of the Epitope Map of Important Influenza A Virus Strains

Fan, S.Wu, Y.Wang, S.Wang, Z.Jiang, B.Liu, Y.Liang, R.Zhou, W.Zhang, N.Xia, C.

(2016) J.Virol. 90: 6625-6641

  • DOI: 10.1128/JVI.00119-16

  • PubMed Abstract: 
  • The lack of a peptide-swine leukocyte antigen class I (pSLA I) complex structure presents difficulties for the study of swine cytotoxic T lymphocyte (CTL) immunity and molecule vaccine development to eliminate important swine viral diseases, such as ...

    The lack of a peptide-swine leukocyte antigen class I (pSLA I) complex structure presents difficulties for the study of swine cytotoxic T lymphocyte (CTL) immunity and molecule vaccine development to eliminate important swine viral diseases, such as influenza A virus (IAV). Here, after cloning and comparing 28 SLA I allelic genes from Chinese Heishan pigs, pSLA-3*hs0202 was crystalized and solved. SLA-3*hs0202 binding with sβ2m and a KMNTQFTAV (hemagglutinin [HA]-KMN9) peptide from the 2009 pandemic swine H1N1 strain clearly displayed two distinct conformations with HA-KMN9 peptides in the structures, which are believed to be beneficial to stimulate a broad spectrum of CTL immune responses. Notably, we found that different HA-KMN9 conformations are caused, not only by the flexibility of the side chains of residues in the peptide-binding groove (PBG), but also by the skewing of α1 and α2 helixes forming the PBG. In addition, alanine scanning and circular-dichroism (CD) spectra confirmed that the B, D, and F pockets play critical biochemical roles in determining the peptide-binding motif of SLA-3*hs0202. Based on biochemical parameters and comparisons to similar pockets in other known major histocompatibility complex class I (MHC-I) structures, the fundamental motif for SLA-3*hs0202 was determined to be X-(M/A/R)-(N/Q/R/F)-X-X-X-X-X-(V/I) by refolding in vitro and multiple mutant peptides. Finally, 28 SLA-3*hs0202-restricted epitope candidates were identified from important IAV strains, and two of them have been found in humans as HLA-A*0201-specific IAV epitopes. Structural and biochemical illumination of pSLA-3*hs0202 can benefit vaccine development to control IAV in swine.


    Organizational Affiliation

    Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China.,Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China zhangnianzhi@cau.edu.cn xiachun@cau.edu.cn.,Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, China Agricultural University, Beijing, China.,College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, People's Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MHC class I antigen
A, D
275Sus scrofaMutation(s): 0 
Gene Names: SLA-1
Find proteins for A0A0N9JT91 (Sus scrofa)
Go to UniProtKB:  A0A0N9JT91
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B, E
98Sus scrofaMutation(s): 0 
Gene Names: B2M
Find proteins for Q07717 (Sus scrofa)
Go to Gene View: B2M
Go to UniProtKB:  Q07717
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Nonapeptide from Influenza A virus HA protein
C, F
9Influenza A virusMutation(s): 0 
Gene Names: HA
Find proteins for C4RUF0 (Influenza A virus)
Go to UniProtKB:  C4RUF0
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.150 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 206.453α = 90.00
b = 41.471β = 117.46
c = 106.735γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXphasing
PHASERdata scaling
HKL-2000data reduction
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The 863 Project of the China Ministry of Science and TechnologyChinaNo. 2013AA102503

Revision History 

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-05-25
    Type: Database references
  • Version 1.2: 2016-07-27
    Type: Database references
  • Version 1.3: 2017-10-04
    Type: Data collection, Database references, Derived calculations