2OL3

crystal structure of BM3.3 ScFV TCR in complex with PBM8-H-2KBM8 MHC class I molecule


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

How much can a T-cell antigen receptor adapt to structurally distinct antigenic peptides?

Mazza, C.Auphan-Anezin, N.Gregoire, C.Guimezanes, A.Kellenberger, C.Roussel, A.Kearney, A.van der Merwe, P.A.Schmitt-Verhulst, A.M.Malissen, B.

(2007) Embo J. 26: 1972-1983

  • DOI: 10.1038/sj.emboj.7601605

  • PubMed Abstract: 
  • Binding degeneracy is thought to constitute a fundamental property of the T-cell antigen receptor (TCR), yet its structural basis is poorly understood. We determined the crystal structure of a complex involving the BM3.3 TCR and a peptide (pBM8) boun ...

    Binding degeneracy is thought to constitute a fundamental property of the T-cell antigen receptor (TCR), yet its structural basis is poorly understood. We determined the crystal structure of a complex involving the BM3.3 TCR and a peptide (pBM8) bound to the H-2K(bm8) major histocompatibility complex (MHC) molecule, and compared it with the structures of the BM3.3 TCR bound to H-2K(b) molecules loaded with two peptides that had a minimal level of primary sequence identity with pBM8. Our findings provide a refined structural view of the basis of BM3.3 TCR cross-reactivity and a structural explanation for the long-standing paradox that a TCR antigen-binding site can be both specific and degenerate. We also measured the thermodynamic features and biological penalties that incurred during cross-recognition. Our data illustrate the difficulty for a given TCR in adapting to distinct peptide-MHC surfaces while still maintaining affinities that result in functional in vivo responses. Therefore, when induction of protective effector T cells is used as the ultimate criteria for adaptive immunity, TCRs are probably much less degenerate than initially assumed.


    Organizational Affiliation

    Centre d'Immunologie de Marseille-Luminy, Université de la Méditerrannée, 13288 Marseille Cedex 09, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BM3.3 T-CELL RECEPTOR ALPHA-CHAIN
A
142Mus musculusMutation(s): 0 
Gene Names: TRADV16D (TRAV16)
Find proteins for Q5R1F1 (Mus musculus)
Go to UniProtKB:  Q5R1F1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BM3.3 T-CELL RECEPTOR BETA-CHAIN
B
113Mus musculusMutation(s): 0 
Find proteins for P04214 (Mus musculus)
Go to UniProtKB:  P04214
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ALLOGENEIC H-2KBM8 MHC CLASS I MOLECULE
H
279Mus musculusMutation(s): 0 
Gene Names: H2-K1 (H2-K)
Find proteins for P01901 (Mus musculus)
Go to UniProtKB:  P01901
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
L
100Mus musculusMutation(s): 0 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
NATURALLY PROCESSED OCTAPEPTIDE PBM8
P
8Mus musculusMutation(s): 0 
Gene Names: Rbm5 (Luca15)
Find proteins for Q91YE7 (Mus musculus)
Go to UniProtKB:  Q91YE7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.224 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 102.523α = 90.00
b = 102.523β = 90.00
c = 198.381γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data scaling
REFMACrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-04-03
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance