8KB1

Crystal structure of 11JD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

The impact of micropolymorphism in Anpl-UAA on structural stability and peptide presentation.

Tang, Z.Wang, S.Du, L.Hu, D.Chen, X.Zheng, H.Ding, H.Chen, S.Zhang, L.Zhang, N.

(2024) Int J Biol Macromol 267: 131665-131665

  • DOI: https://doi.org/10.1016/j.ijbiomac.2024.131665
  • Primary Citation of Related Structures:  
    8KB0, 8KB1

  • PubMed Abstract: 

    Micropolymorphism significantly shapes the peptide-binding characteristics of major histocompatibility complex class I (MHC-I) molecules, affecting the host's resistance to pathogens, which is particularly pronounced in avian species displaying the "minimal essential MHC" expression pattern. In this study, we compared two duck MHC-I alleles, Anpl-UAA*77 and Anpl-UAA*78, that exhibit markedly different peptide binding properties despite their high sequence homology. Through mutagenesis experiments and crystallographic analysis of complexes with the influenza virus-derived peptide AEAIIVAMV (AEV9), we identified a critical role for the residue at position 62 in regulating hydrogen-bonding interactions between the peptide backbone and the peptide-binding groove. This modulation affects the characteristics of the B pocket and the stability of the loop region between the 3 10 helix and the α1 helix, leading to significant changes in the structure and stability of the peptide-MHC-I complex (pMHC-I). Moreover, the proportion of different residues at position 62 among Anpl-UAAs may reflect the correlation between pAnpl-UAA stability and duck body temperature. This research not only advances our understanding of the Anpl-UAA structure but also deepens our insight into the impact of MHC-I micropolymorphism on peptide binding.


  • Organizational Affiliation

    National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MHC class I antigen271Anas platyrhynchosMutation(s): 0 
Gene Names: Anpl-UAA
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta2-microglobulin103Anas platyrhynchosMutation(s): 0 
Gene Names: b2m
UniProt
Find proteins for Q14U75 (Anas platyrhynchos)
Explore Q14U75 
Go to UniProtKB:  Q14U75
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14U75
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
peptide of AIV9unidentified influenza virusMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.216 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.593α = 90
b = 87.593β = 90
c = 119.023γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
autoPROCdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32172871

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-29
    Type: Initial release