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 5GSX | pdb_00005gsx

Mouse MHC class I H-2Kd with a MERS-CoV-derived peptide 142-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.242 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5GSX

This is version 1.1 of the entry. See complete history. 

Literature

Protective T Cell Responses Featured by Concordant Recognition of Middle East Respiratory Syndrome Coronavirus-Derived CD8+ T Cell Epitopes and Host MHC.

Liu, W.J., Lan, J., Liu, K., Deng, Y., Yao, Y., Wu, S., Chen, H., Bao, L., Zhang, H., Zhao, M., Wang, Q., Han, L., Chai, Y., Qi, J., Zhao, J., Meng, S., Qin, C., Gao, G.F., Tan, W.

(2017) J Immunol 198: 873-882

  • DOI: https://doi.org/10.4049/jimmunol.1601542
  • Primary Citation Related Structures: 
    5GR7, 5GSB, 5GSR, 5GSV, 5GSX

  • PubMed Abstract: 

    The coordinated recognition of virus-derived T cell epitopes and MHC molecules by T cells plays a pivotal role in cellular immunity-mediated virus clearance. It has been demonstrated that the conformation of MHC class I (MHC I) molecules can be adjusted by the presented peptide, which impacts T cell activation. However, it is still largely unknown whether the conformational shift of MHC I influences the protective effect of virus-specific T cells. In this study, utilizing the Middle East respiratory syndrome coronavirus-infected mouse model, we observed that through the unusual secondary anchor Ile5, a CD8 + T cell epitope drove the conformational fit of Trp 73 on the α1 helix of murine MHC I H-2K d In vitro renaturation and circular dichroism assays indicated that this shift of the structure did not influence the peptide/MHC I binding affinity. Nevertheless, the T cell recognition and the protective effect of the peptide diminished when we made an Ile to Ala mutation at position 5 of the original peptide. The molecular bases of the concordant recognition of T cell epitopes and host MHC-dependent protection were demonstrated through both crystal structure determination and tetramer staining using the peptide-MHC complex. Our results indicate a coordinated MHC I/peptide interaction mechanism and provide a beneficial reference for T cell-oriented vaccine development against emerging viruses such as Middle East respiratory syndrome coronavirus.


  • Organizational Affiliation: 
    • College of Laboratory Medicine and Life Sciences, Institute of Medical Virology, Wenzhou Medical University, Wenzhou 325035, China.

Macromolecule Content 

  • Total Structure Weight: 89.76 kDa 
  • Atom Count: 6,509 
  • Modeled Residue Count: 766 
  • Deposited Residue Count: 766 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
H-2 class I histocompatibility antigen, K-D alpha chain
A, D
274Mus musculusMutation(s): 0 
Gene Names: H2-K1, H2-K
UniProt
Find proteins for P01902 (Mus musculus)
Explore P01902 
Go to UniProtKB:  P01902
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01902
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, E
99Homo sapiensMutation(s): 0 
Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups
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UniProt GroupP61769
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
10-mer peptide from Spike protein
C, F
10Middle East respiratory syndrome-related coronavirusMutation(s): 0 
UniProt
Find proteins for K9N5Q8 (Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012))
Explore K9N5Q8 
Go to UniProtKB:  K9N5Q8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK9N5Q8
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.242 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.623α = 90
b = 68.474β = 106.76
c = 145.075γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CNSdata reduction
CNSdata scaling
PHASESphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Database references, Structure summary