6GB7

Structure of H-2Db with scoop loop from tapasin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 

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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 chainACEG338Mus musculusMutation(s): 0 
Gene Names: H2-D1
Find proteins for P01899 (Mus musculus)
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Go to UniProtKB:  P01899
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinBDH100Mus musculusMutation(s): 1 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
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NIH Common Fund Data Resources
IMPC  MGI:88127
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinF99Mus musculusMutation(s): 1 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
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Go to UniProtKB:  P01887
NIH Common Fund Data Resources
IMPC  MGI:88127
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
PHE-ALA-PRO-GLY-ASN-TYR-PROIJKL7Murine respirovirusMutation(s): 0 
Find proteins for O57286 (Sendai virus (strain Ohita))
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Go to UniProtKB:  O57286
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
GLY-GLY-LEU-SERPR10Mus musculusMutation(s): 0 
Gene Names: TapbpTapa
Find proteins for Q9R233 (Mus musculus)
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Go to UniProtKB:  Q9R233
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.7α = 90
b = 123.86β = 103.66
c = 100.11γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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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