6KVM | pdb_00006kvm

Crystal structure of Chicken MHC Class II for 1.9 angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.227 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.206 (DCC) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

A Newly Recognized Pairing Mechanism of the alpha- and beta-Chains of the Chicken Peptide-MHC Class II Complex.

Zhang, L.Li, X.Ma, L.Zhang, B.Meng, G.Xia, C.

(2020) J Immunol 204: 1630-1640

  • DOI: https://doi.org/10.4049/jimmunol.1901305
  • Primary Citation Related Structures: 
    6KVM

  • PubMed Abstract: 

    MHC class II (MHC-II) molecules play a crucial role in cellular and humoral immunity by forming peptide-MHC-II (pMHC-II) complexes. The three-dimensional structures of pMHC-II complexes have been well resolved in humans and mice. However, there is no structural information for pMHC-II complexes in nonmammals. In chickens, there are two closely related and highly polymorphic β-chains and one monomorphic α-chain, and the mechanism by which one monomorphic α-chain combines with two polymorphic β-chains to form a functional heterodimer remains unknown. In this study, we report the crystal structure of a chicken pMHC-II complex (pBL2*019:01) at 1.9-Å resolution as the first nonmammalian structure of a pMHC-II complex. The structure reveals an increase in hydrogen bonding between the α and β main chains at the central interface that is introduced by the insertion of four residues in the α-chain. The residues in the β-chain that form hydrogen bonds with the α-chain are conserved among all β alleles. These structural characteristics explain the phenomenon of only one BLA allele without sequence variation pairing with highly diverse BLB alleles from two loci in the genome. Additionally, the characteristics of the peptide in the peptide-binding groove were confirmed. These results provide a new understanding of the pairing mechanism of the α- and β-chains in a pMHC-II complex and establish a structural principle to design epitope-related vaccines for the prevention of chicken diseases.


  • Organizational Affiliation
    • Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing 100193, China; and.

Macromolecule Content 

  • Total Structure Weight: 48.22 kDa 
  • Atom Count: 3,317 
  • Modeled Residue Count: 380 
  • Deposited Residue Count: 425 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MHC class II alpha chain194Gallus gallusMutation(s): 0 
Gene Names: B-LA
UniProt
Find proteins for Q4U5Z6 (Gallus gallus)
Explore Q4U5Z6 
Go to UniProtKB:  Q4U5Z6
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UniProt GroupQ4U5Z6
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
MHC class II beta chain 2214Gallus gallusMutation(s): 0 
Gene Names: B-LBBLB2
UniProt
Find proteins for Q4U600 (Gallus gallus)
Explore Q4U600 
Go to UniProtKB:  Q4U600
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UniProt GroupQ4U600
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
peptide from 60S ribosomal protein L3017Gallus gallusMutation(s): 0 
Gene Names: RPL30
UniProt
Find proteins for P67883 (Gallus gallus)
Explore P67883 
Go to UniProtKB:  P67883
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UniProt GroupP67883
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.227 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.206 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.397α = 90
b = 57.297β = 110.676
c = 58.057γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)ChinaNo.31972683
National Natural Science Foundation of China (NSFC)ChinaNo.31572493

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2020-07-08
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary