3HG1

Germline-governed recognition of a cancer epitope by an immunodominant human T cell receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Germ line-governed recognition of a cancer epitope by an immunodominant human T-cell receptor.

Cole, D.K.Yuan, F.Rizkallah, P.J.Miles, J.J.Gostick, E.Price, D.A.Gao, G.F.Jakobsen, B.K.Sewell, A.K.

(2009) J.Biol.Chem. 284: 27281-27289

  • DOI: 10.1074/jbc.M109.022509

  • PubMed Abstract: 
  • CD8(+) T-cells specific for MART-1-(26-35), a dominant melanoma epitope restricted by human leukocyte antigen (HLA)-A*0201, are exceptionally common in the naive T-cell repertoire. Remarkably, the TRAV12-2 gene is used to encode the T-cell receptor a ...

    CD8(+) T-cells specific for MART-1-(26-35), a dominant melanoma epitope restricted by human leukocyte antigen (HLA)-A*0201, are exceptionally common in the naive T-cell repertoire. Remarkably, the TRAV12-2 gene is used to encode the T-cell receptor alpha (TCRalpha) chain in >87% of these T-cells. Here, the molecular basis for this genetic bias is revealed from the structural and thermodynamic properties of an archetypal TRAV12-2-encoded TCR complexed to the clinically relevant heteroclitic peptide, ELAGIGILTV, bound to HLA-A*0201 (A2-ELA). Unusually, the TRAV12-2 germ line-encoded regions of the TCR dominate the major atomic contacts with the peptide at the TCR/A2-ELA interface. This "innate" pattern of antigen recognition probably explains the unique characteristics and extraordinary frequencies of CD8(+) T-cell responses to this epitope.


    Organizational Affiliation

    Department of Infection, Immunity, and Biochemistry, Henry Wellcome Building, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MHC class I antigen
A
276Homo sapiensMutation(s): 0 
Gene Names: HLA-A
Find proteins for Q8WLS4 (Homo sapiens)
Go to Gene View: HLA-A
Go to UniProtKB:  Q8WLS4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
100Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
CANCER/MART-1
C
10Homo sapiensMutation(s): 0 
Gene Names: MLANA (MART1)
Find proteins for Q16655 (Homo sapiens)
Go to Gene View: MLANA
Go to UniProtKB:  Q16655
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
T-CELL RECEPTOR, ALPHA CHAIN
D
194Homo sapiensMutation(s): 0 
Gene Names: TRAC (TCRA)
Find proteins for P01848 (Homo sapiens)
Go to UniProtKB:  P01848
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
T-cell Receptor, Beta Chain
E
244Homo sapiensMutation(s): 0 
Gene Names: TRBC1
Find proteins for P01850 (Homo sapiens)
Go to UniProtKB:  P01850
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, E
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.225 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 120.898α = 90.00
b = 120.898β = 90.00
c = 81.980γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
MOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2014-04-09
    Type: Source and taxonomy