2H6P

Crystal structure of HLA-B*3501 presenting the human cytochrome P450 derived peptide, KPIVVLHGY

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

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


Literature

Alloreactivity between disparate cognate and allogeneic pMHC-I complexes is the result of highly focused, peptide-dependent structural mimicry

Archbold, J.K., Macdonald, W.A., Miles, J.J., Brennan, R.M., Kjer-Nielsen, L., McCluskey, J., Burrows, S.R., Rossjohn, J.

(2006) J Biol Chem 281: 34324-34332

  • DOI: 10.1074/jbc.M606755200
  • Primary Citation of Related Structures:  
    2H6P

  • PubMed Abstract: 

    • Our understanding of the molecular mechanisms of T cell alloreactivity remains limited by the lack of systems for which both the T cell receptor allo- and cognate ligand are known. Here we provide evidence that a single alloreactive T cell receptor inter ...

    Our understanding of the molecular mechanisms of T cell alloreactivity remains limited by the lack of systems for which both the T cell receptor allo- and cognate ligand are known. Here we provide evidence that a single alloreactive T cell receptor interacts with analogous structural regions of its cognate ligand, HLA-B*0801(FLRGRAYGL), as its allogeneic ligand, HLA-B*3501(KPIVVLHGY). The crystal structures of the binary peptide-major histocompatibility complexes show marked differences in the conformation of the heavy chains as well as the bound peptides. Nevertheless, both epitopes possess a prominent solvent-exposed aromatic residue at position 7 flanked by a small glycine at position 8 of the peptide determinant. Moreover, regions of close structural homology between the heavy chains of HLA B8 and HLA B35 coincided with regions that have previously been implicated in "hot spots" of T cell receptor recognition. The avidity of this human T cell receptor was also comparable for the allo- and cognate ligand, consistent with the modes of T cell receptor binding being broadly similar for these complexes. Collectively, it appears that highly focused structural mimicry against a diverse structural background provides a basis for the observed alloreactivity in this system. This cross-reactivity underpins the T cell degeneracy inherent in the limited mature T cell repertoire that must respond to a vast diversity of microbial antigens.

    Organizational Affiliation: 

    Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA-B35 A276Homo sapiensMutation(s): 0 
Gene Names: HLA-B, HLAB
Find proteins for P01889 (Homo sapiens)
Explore P01889 
Go to UniProtKB:  P01889
NIH Common Fund Data Resources
PHAROS:  P01889
GTEx:  ENSG00000234745
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulin B99Homo sapiensMutation(s): 0 
Gene Names: B2M, CDABP0092, HDCMA22P
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS:  P61769
GTEx:  ENSG00000166710
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
9 mer peptide from Cytochrome P450 C9N/AMutation(s): 0 
Find proteins for P33260 (Homo sapiens)
Explore P33260 
Go to UniProtKB:  P33260
NIH Common Fund Data Resources
PHAROS:  P33260
GTEx:  ENSG00000108242
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.279α = 90
b = 82.07β = 90
c = 109.881γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-09-19
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance