6LBE

Crystal structure of bony fish MHC class I binding beta2M-2 for 2.6 angstrom

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.173 

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Literature

The Mechanism of beta 2m Molecule-Induced Changes in the Peptide Presentation Profile in a Bony Fish.

Li, Z., Zhang, N., Ma, L., Zhang, L., Meng, G., Xia, C.

(2020) iScience 23: 101119-101119

  • DOI: 10.1016/j.isci.2020.101119
  • Primary Citation of Related Structures:  
    6LBE, 5H5Z

  • PubMed Abstract: 

    • Contemporary antigen presentation knowledge is based on the existence of a single β2m locus, and a classical MHC class I forms a complex with a peptide (i.e., pMHC-I) to trigger CTL immunity. However, two β2m loci have been found in diploid bony fish ...

    Contemporary antigen presentation knowledge is based on the existence of a single β2m locus, and a classical MHC class I forms a complex with a peptide (i.e., pMHC-I) to trigger CTL immunity. However, two β2m loci have been found in diploid bony fish; the function of the two β2m molecules is unclear. Here, we determined the variant peptide profiles originating from different products of the β2m loci binding to the same MHC-I molecule and further solved the crystal structures of the two pMHC-I molecules (i.e., pCtid-UAA-β2m-2 and pCtid-UAA-β2m-1-II). Of note, in pCtid-UAA-β2m-2, a unique hydrogen bond network formed in the bottom of the peptide-binding groove (PBG) led to α2-helix drift, ultimately leading to structural changes in the PBG. The mechanism of the change in peptide presentation profiles by β2m molecules is illustrated. The results are also of great significance for antivirus and antitumor functions in cold-blooded vertebrates and even humans.

    Organizational Affiliation: 

    Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China. Electronic address: xiachun@cau.edu.cn.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MHC class I antigenA, C275Ctenopharyngodon idellaMutation(s): 0 
Gene Names: UAA106
Find proteins for Q65XY8 (Ctenopharyngodon idella)
Explore Q65XY8 
Go to UniProtKB:  Q65XY8
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB, D99Ctenopharyngodon idellaMutation(s): 0 
Gene Names: b2m-b
Find proteins for A0A3G2VUI3 (Ctenopharyngodon idella)
Explore A0A3G2VUI3 
Go to UniProtKB:  A0A3G2VUI3
Protein Feature View
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
9-mer peptide from RNA-DIRECTED RNA POLYMERASE LE, F9synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.173 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.19α = 64.94
b = 65.27β = 75.67
c = 69.71γ = 73.61
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-11-14 
  • Released Date: 2020-11-04 
    • Deposition Author(s): Li, Z.B., Xia, C.
Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChinaGrant 31572653

Revision History 

  • Version 1.0: 2020-11-04
    Type: Initial release