3KXF

Crystal Structure of SB27 TCR in complex with the 'restriction triad' mutant HLA-B*3508-13mer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Hard wiring of T cell receptor specificity for the major histocompatibility complex is underpinned by TCR adaptability

Burrows, S.R.Chen, Z.Archbold, J.K.Tynan, F.E.Beddoe, T.Kjer-Nielsen, L.Miles, J.J.Khanna, R.Moss, D.J.Liu, Y.C.Gras, S.Kostenko, L.Brennan, R.M.Clements, C.S.Brooks, A.G.Purcell, A.W.McCluskey, J.Rossjohn, J.

(2010) Proc Natl Acad Sci U S A 107: 10608-10613

  • DOI: 10.1073/pnas.1004926107
  • Primary Citation of Related Structures:  
    3KWW, 3KXF

  • PubMed Abstract: 
  • alphabeta T cell receptors (TCRs) are genetically restricted to corecognize peptide antigens bound to self-major histocompatibility complex (pMHC) molecules; however, the basis for this MHC specificity remains unclear. Despite the current dogma, eval ...

    alphabeta T cell receptors (TCRs) are genetically restricted to corecognize peptide antigens bound to self-major histocompatibility complex (pMHC) molecules; however, the basis for this MHC specificity remains unclear. Despite the current dogma, evaluation of the TCR-pMHC-I structural database shows that the nongermline-encoded complementarity-determining region (CDR)-3 loops often contact the MHC-I, and the germline-encoded CDR1 and -2 loops frequently participate in peptide-mediated interactions. Nevertheless, different TCRs adopt a roughly conserved docking mode over the pMHC-I, in which three MHC-I residues (65, 69, and 155) are invariably contacted by the TCR in one way or another. Nonetheless, the impact of mutations at these three positions, either individually or together, was not uniformly detrimental to TCR recognition of pHLA-B*0801 or pHLA-B*3508. Moreover, when TCR-pMHC-I recognition was impaired, this could be partially restored by expression of the CD8 coreceptor. The structure of a TCR-pMHC-I complex in which these three (65, 69, and 155) MHC-I positions were all mutated resulted in shifting of the TCR footprint relative to the cognate complex and formation of compensatory interactions. Collectively, our findings reveal the inherent adaptability of the TCR in maintaining peptide recognition while accommodating changes to the central docking site on the pMHC-I.


    Organizational Affiliation

    Cellular Immunology Laboratory, Queensland Institute of Medical Research and Australian Centre for Vaccine Development, Brisbane 4029, Australia.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, B-35 alpha chainACIK276Homo sapiensMutation(s): 3 
Gene Names: HLA-BHLAB
Find proteins for P01889 (Homo sapiens)
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PHAROS  P01889
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinBFJL99Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
Find proteins for P61769 (Homo sapiens)
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PHAROS  P61769
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
SB27 T cell receptor alpha chainDGMN204Homo sapiensMutation(s): 0 
Gene Names: TRACTCRA
Find proteins for P01848 (Homo sapiens)
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PHAROS  P01848
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
SB27 T cell receptor beta chainEHOP241Homo sapiensMutation(s): 0 
Gene Names: TRBC2TCRBC2
Find proteins for A0A5B9 (Homo sapiens)
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Go to UniProtKB:  A0A5B9
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PHAROS  A0A5B9
Protein Feature View
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
peptide from Trans-activator protein BZLF1QRST13N/AMutation(s): 0 
Find proteins for P03206 (Epstein-Barr virus (strain B95-8))
Explore P03206 
Go to UniProtKB:  P03206
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, P
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.69α = 90
b = 207.077β = 90.19
c = 123.512γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-02-26
    Changes: Database references