6GB5

Structure of H-2Db with truncated SEV peptide and GL

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Successive crystal structure snapshots suggest the basis for MHC class I peptide loading and editing by tapasin.

Hafstrand, I., Sayitoglu, E.C., Apavaloaei, A., Josey, B.J., Sun, R., Han, X., Pellegrino, S., Ozkazanc, D., Potens, R., Janssen, L., Nilvebrant, J., Nygren, P.A., Sandalova, T., Springer, S., Georgoudaki, A.M., Duru, A.D., Achour, A.

(2019) Proc Natl Acad Sci U S A 116: 5055-5060

  • DOI: 10.1073/pnas.1807656116
  • Primary Citation of Related Structures:  
    6GB6, 6GB5, 6GB7

  • PubMed Abstract: 

    • MHC-I epitope presentation to CD8 + T cells is directly dependent on peptide loading and selection during antigen processing. However, the exact molecular bases underlying peptide selection and binding by MHC-I remain largely unknown. Wit ...

    MHC-I epitope presentation to CD8 + T cells is directly dependent on peptide loading and selection during antigen processing. However, the exact molecular bases underlying peptide selection and binding by MHC-I remain largely unknown. Within the peptide-loading complex, the peptide editor tapasin is key to the selection of MHC-I-bound peptides. Here, we have determined an ensemble of crystal structures of MHC-I in complex with the peptide exchange-associated dipeptide GL, as well as the tapasin-associated scoop loop, alone or in combination with candidate epitopes. These results combined with mutation analyses allow us to propose a molecular model underlying MHC-I peptide selection by tapasin. The N termini of bound peptides most probably bind first in the N-terminal and middle region of the MHC-I peptide binding cleft, upon which the peptide C termini are tested for their capacity to dislodge the tapasin scoop loop from the F pocket of the MHC-I cleft. Our results also indicate important differences in peptide selection between different MHC-I alleles.

    Organizational Affiliation: 

    Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, SE-17176 Stockholm, Sweden; adnane.achour@ki.se.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
H-2 class I histocompatibility antigen, D-B alpha chainA, C338Mus musculusMutation(s): 0 
Gene Names: H2-D1
Find proteins for P01899 (Mus musculus)
Explore P01899 
Go to UniProtKB:  P01899
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB, D99Mus musculusMutation(s): 1 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
Explore P01887 
Go to UniProtKB:  P01887
NIH Common Fund Data Resources
IMPC  MGI:88127
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PHE-ALA-PRO-GLY-ASN-TYR-PROE, F7Murine respirovirusMutation(s): 0 
Find proteins for O57286 (Sendai virus (strain Ohita))
Explore O57286 
Go to UniProtKB:  O57286
Protein Feature View
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
GLY-LEUG, H2Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.93α = 90
b = 123.36β = 103.73
c = 99.206γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-03-06
    Type: Initial release
  • Version 1.1: 2019-03-13
    Changes: Data collection, Database references
  • Version 1.2: 2019-03-20
    Changes: Data collection, Database references