2AK4 | pdb_00002ak4

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 (Depositor), 0.284 (DCC) 
  • R-Value Work: 
    0.246 (Depositor), 0.266 (DCC) 
  • R-Value Observed: 
    0.247 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 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: https://doi.org/10.1038/ni1257
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 390.03 kDa 
  • Atom Count: 26,609 
  • Modeled Residue Count: 3,329 
  • Deposited Residue Count: 3,376 
  • Unique protein chains: 5

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HLA-B35 variantA,
F,
K,
P [auth Q]
276Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
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PHAROS:  P01889
GTEx:  ENSG00000234745 
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UniProt GroupP01889
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulinB,
G,
L,
Q [auth R]
99Homo sapiensMutation(s): 0 
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PHAROS:  P61769
GTEx:  ENSG00000166710 
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UniProt GroupP61769
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
EBV peptide LPEPLPQGQLTAYC,
H,
M,
R [auth S]
13N/AMutation(s): 0 
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
SB27 T cell receptor alpha chainD,
I,
N,
S [auth T]
211Homo sapiensMutation(s): 0 
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
SB27 T cell receptor beta chainE,
J,
O [auth P],
T [auth U]
245Homo sapiensMutation(s): 0 
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UniProt GroupP01850
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / 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]
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.278 (Depositor), 0.284 (DCC) 
  • R-Value Work:  0.246 (Depositor), 0.266 (DCC) 
  • R-Value Observed: 0.247 (Depositor) 
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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Entry History 

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
  • Version 1.3: 2024-10-23
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary