5H5Z

Crystal structure of bony fish MHC class I, peptide and B2m II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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:  
    5H5Z, 6LBE

  • 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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MHC class I antigenA275Ctenopharyngodon idellaMutation(s): 0 
Gene Names: UAA106
Find proteins for Q65XY8 (Ctenopharyngodon idella)
Explore Q65XY8 
Go to UniProtKB:  Q65XY8
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB98Ctenopharyngodon idellaMutation(s): 1 
Gene Names: B2m
Find proteins for Q6L7B0 (Ctenopharyngodon idella)
Explore Q6L7B0 
Go to UniProtKB:  Q6L7B0
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
peptide chainC9Carp sprivivirusMutation(s): 0 
Gene Names: L
EC: 2.7.7.48 (UniProt), 2.1.1.56 (UniProt), 2.7.7.88 (UniProt), 2.1.1.296 (UniProt)
Find proteins for Q91DR9 (Spring viremia of carp virus)
Explore Q91DR9 
Go to UniProtKB:  Q91DR9
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.35α = 90
b = 50.65β = 129.37
c = 90.31γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMACrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
the State Key Program of the National Natural Science Foundation of ChinaChina31230074
the 973 Project of the China Ministry of Science and TechnologyChina2013CB835302

Revision History 

  • Version 1.0: 2017-11-22
    Type: Initial release
  • Version 1.1: 2020-11-04
    Changes: Database references