9UL1 | pdb_00009ul1

Crystal structure of Tibetan wild boar SLA-1*Z0301 for 2.32 angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 
    0.294 (Depositor), 0.306 (DCC) 
  • R-Value Work: 
    0.278 (Depositor), 0.281 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Literature

Structural basis of Tibetan wild boar SLA-1*Z0301 reveals conserved peptide presentation and potential high-altitude adaptation.

Fan, S.Kang, C.Peng, J.Wang, T.Ren, S.Li, J.Li, L.Wu, C.Wang, Y.Li, L.

(2025) Int J Biol Macromol 320: 145933-145933

  • DOI: https://doi.org/10.1016/j.ijbiomac.2025.145933
  • Primary Citation Related Structures: 
    9UL1

  • PubMed Abstract: 

    Major Histocompatibility Complex (MHC) class I molecules facilitate antiviral immunity through their polymorphic peptide-binding diversity. Tibetan wild boars, adapted to extreme plateau conditions, exhibit enhanced disease resistance. Here, we present the first three-dimensional structure of the Tibetan wild boar SLA-1*Z0301 in complex with the GP3-ALL9 peptide derived from porcine reproductive and respiratory syndrome virus (PRRSV). Using X-ray crystallography and AlphaFold3 modeling, we characterized the peptide-binding motif of SLA-1*Z0301, which shares conserved binding pockets with SLA-1*08 alleles found in various domestic pigs, indicating convergent peptide presentation across wild and domestic swine lineages. Thermal stability assays revealed that the primary anchors of SLA-1*Z0301-P2 (B pocket, Tm = 42.5 °C) and P9 (F pocket, Tm = 47.6 °C)-exhibited greater stability compared to mutants in the Heishan pig SLA-3*hs0202 (P3-A = 40.0 °C, P9-A = 38.3 °C), suggesting structural adaptations to high-altitude conditions. A genome-wide screening identified 125 nonapeptides from PRRSV-1 and PRRSV-2 that conform to the SLA-1*Z0301 motif, spanning structural (GP2-GP5) and nonstructural proteins. Notably, five epitopes overlapped with immunodominant responses observed in Large White and Yorkshire × Landrace, highlighting conserved antigen presentation across wild and domestic swine lineages. These results provide valuable insights into the development of cross-species antiviral strategies and vaccine design.


  • Organizational Affiliation
    • College of Life Sciences and Agronomy, Zhoukou Normal University, Zhoukou, China; Institute of Neuroscience and Translational Medicine, Zhoukou Normal University, Zhoukou, China. Electronic address: fanshuhuayan@cau.edu.cn.

Macromolecule Content 

  • Total Structure Weight: 44.22 kDa 
  • Atom Count: 3,118 
  • Modeled Residue Count: 382 
  • Deposited Residue Count: 382 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MHC class I antigen276Sus scrofaMutation(s): 0 
Gene Names: SLA-1
UniProt
Find proteins for A0A286S063 (Sus scrofa)
Explore A0A286S063 
Go to UniProtKB:  A0A286S063
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A286S063
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulin97Sus scrofaMutation(s): 0 
Gene Names: B2M
UniProt
Find proteins for Q07717 (Sus scrofa)
Explore Q07717 
Go to UniProtKB:  Q07717
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07717
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ALA-LEU-LEU-SER-SER-LYS-THR-SER-VAL9Porcine reproductive and respiratory syndrome virusMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free:  0.294 (Depositor), 0.306 (DCC) 
  • R-Value Work:  0.278 (Depositor), 0.281 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.806α = 90
b = 48.428β = 100.466
c = 53.419γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31702232

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-13
    Type: Initial release