6M2J

Uncommon structural features of rabbit MHC class I (RLA-A1) complexed with rabbit haemorrhagic disease virus (RHDV) derived peptide, VP60-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

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Literature

Strict Assembly Restriction of Peptides from Rabbit Hemorrhagic Disease Virus Presented by Rabbit Major Histocompatibility Complex Class I Molecule RLA-A1.

Zhang, Q.Liu, K.Yue, C.Zhang, D.Lu, D.Xiao, W.Liu, P.Zhao, Y.Gao, G.Ding, C.Lyu, J.Liu, W.J.

(2020) J Virol 94

  • DOI: 10.1128/JVI.00396-20
  • Primary Citation of Related Structures:  
    6M24, 6M2K, 6M2J

  • PubMed Abstract: 
  • Rabbits are pivotal domestic animals for both the economy and as an animal model for human diseases. A large number of rabbits have been infected by rabbit hemorrhagic disease virus (RHDV) in natural and artificial pandemics in the past. Differences ...

    Rabbits are pivotal domestic animals for both the economy and as an animal model for human diseases. A large number of rabbits have been infected by rabbit hemorrhagic disease virus (RHDV) in natural and artificial pandemics in the past. Differences in presentation of antigenic peptides by polymorphic major histocompatibility complex (MHC) molecules to T-cell receptors (TCR) on T lymphocytes are associated with viral clearance in mammals. Herein, we screened and identified a series of peptides derived from RHDV binding to the rabbit MHC class I molecule, RLA-A1. The small, hydrophobic B and F pockets of RLA-A1 capture a peptide motif analogous to that recognized by human class I molecule HLA-A*0201, with more restricted aliphatic anchors at P2 and PΩ positions. Meanwhile, the rabbit molecule is featured with an uncommon residue combination of Gly53, Val55 and Glu56, making the 3 10 helix and the loop between the 3 10 and α1 helices closer to the α2 helix. A wider A pocket in RLA-A1 can induce a special conformation of the P1 anchor and may play a pivotal role in peptide assembly and TCR recognition. Our study broadens the knowledge on T-cell immunity in domestic animals and also provides useful insights for vaccine development to prevent infectious diseases in rabbits. IMPORTANCE We screened rabbit MHC class I RLA-A1-restricted peptides from the capsid protein VP60 of Rabbit haemorrhagic disease virus (RHDV) and determined the structures of RLA-A1 complexed with three peptides, VP60-1, VP60-2 and VP60-10. From the structures, we found that the peptide binding motifs of RLA-A1 are extremely constraining. Thus, there is a generally restricted peptide selection for RLA-A1 compared to human HLA-A*0201. In addition, uncommon residues Gly53, Val55 and Glu56 of RLA-A1 are located between 3 10 helix and α1 helix which makes the steric position of 3 10 helix in RLA-A1 much closer to the α2 helix than other mammalian MHC class I molecules. This special conformation between 3 10 helix and α1 helix plays a pivotal role in rabbit MHC class I assembly. Our results provide new insights into MHC class I molecule assembly and peptide presentation of domestic mammals. Furthermore, these data also broaden our knowledge on T-cell immunity in rabbits and may also provide useful information for vaccine development to prevent infectious diseases in rabbits.


    Organizational Affiliation

    NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RLA class I histocompatibility antigen, alpha chain 19-1A274Oryctolagus cuniculusMutation(s): 0 
Find proteins for P06140 (Oryctolagus cuniculus)
Explore P06140 
Go to UniProtKB:  P06140
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
VP60-1C9Rabbit hemorrhagic disease virusMutation(s): 0 
EC: 3.6.1.15 (UniProt), 3.4.22.66 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P27410 (Rabbit hemorrhagic disease virus (strain Rabbit/Germany/FRG/1989))
Explore P27410 
Go to UniProtKB:  P27410
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.625α = 90
b = 74.361β = 90
c = 155.669γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PROTEUM PLUSdata reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2020-09-02
    Changes: Database references