2AK4

Crystal Structure of SB27 TCR in complex with HLA-B*3508-13mer peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.247 

wwPDB Validation   3D Report Full Report


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


Literature

T cell receptor recognition of a 'super-bulged' major histocompatibility complex class I-bound peptide

Tynan, F.E., Burrows, S.R., Buckle, A.M., Clements, C.S., Borg, N.A., Miles, J.J., Beddoe, T., Whisstock, J.C., Wilce, M.C., Silins, S.L., Burrows, J.M., Kjer-Nielsen, L., Kostenko, L., Purcell, A.W., McCluskey, J., Rossjohn, J.

(2005) Nat Immunol 6: 1114-1122

  • DOI: 10.1038/ni1257
  • Primary Citation of Related Structures:  
    2AK4

  • PubMed Abstract: 

    • Unusually long major histocompatibility complex (MHC) class I-restricted epitopes are important in immunity, but their 'bulged' conformation represents a potential obstacle to alphabeta T cell receptor (TCR)-MHC class I docking. To elucidate how such recognition is achieved while still preserving MHC restriction, we have determined here the structure of a TCR in complex with HLA-B(*)3508 presenting a peptide 13 amino acids in length ...

    Unusually long major histocompatibility complex (MHC) class I-restricted epitopes are important in immunity, but their 'bulged' conformation represents a potential obstacle to alphabeta T cell receptor (TCR)-MHC class I docking. To elucidate how such recognition is achieved while still preserving MHC restriction, we have determined here the structure of a TCR in complex with HLA-B(*)3508 presenting a peptide 13 amino acids in length. This complex was atypical of TCR-peptide-MHC class I interactions, being dominated at the interface by peptide-mediated interactions. The TCR assumed two distinct orientations, swiveling on top of the centrally bulged, rigid peptide such that only limited contacts were made with MHC class I. Although the TCR-peptide recognition resembled an antibody-antigen interaction, the TCR-MHC class I contacts defined a minimal 'generic footprint' of MHC-restriction. Thus our findings simultaneously demonstrate the considerable adaptability of the TCR and the 'shape' of MHC restriction.

    Organizational Affiliation: 

    The 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 variantA, F, K, P [auth Q]276Homo sapiensMutation(s): 0 
Gene Names: HLA-B, HLAB
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PHAROS:  P01889
GTEx:  ENSG00000234745
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB, G, L, Q [auth R]99Homo sapiensMutation(s): 0 
Gene Names: B2M, CDABP0092, HDCMA22P
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GTEx:  ENSG00000166710
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
EBV peptide LPEPLPQGQLTAYC, H, M, R [auth S]13N/AMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
SB27 T cell receptor alpha chainD, I, N, S [auth T]211Homo sapiensMutation(s): 0 
Gene Names: TRAC, TCRA
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
SB27 T cell receptor beta chainE, J, O [auth P], T [auth U]245Homo sapiensMutation(s): 0 
Gene Names: TRBC1
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD
Download Ideal Coordinates CCD File 
AA [auth E] , BA [auth F] , CA [auth F] , DA [auth F] , EA [auth F] , FA [auth G] , GA [auth H] , HA [auth J] , 
AA [auth E],  BA [auth F],  CA [auth F],  DA [auth F],  EA [auth F],  FA [auth G],  GA [auth H],  HA [auth J],  IA [auth K],  JA [auth K],  KA [auth K],  LA [auth L],  MA [auth Q],  NA [auth Q],  OA [auth R],  PA [auth S],  U [auth A],  V [auth A],  W [auth A],  X [auth B],  Y [auth C],  Z [auth D]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.247 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.154α = 90
b = 213.282β = 89.94
c = 122.303γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-10-11
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance