3QIB

Crystal structure of the 2B4 TCR in complex with MCC/I-Ek


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of specificity and cross-reactivity in T cell receptors specific for cytochrome c-I-E(k).

Newell, E.W.Ely, L.K.Kruse, A.C.Reay, P.A.Rodriguez, S.N.Lin, A.E.Kuhns, M.S.Garcia, K.C.Davis, M.M.

(2011) J.Immunol. 186: 5823-5832

  • DOI: 10.4049/jimmunol.1100197
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • T cells specific for the cytochrome c Ag are widely used to investigate many aspects of TCR specificity and interactions with peptide-MHC, but structural information has long been elusive. In this study, we present structures for the well-studied 2B4 ...

    T cells specific for the cytochrome c Ag are widely used to investigate many aspects of TCR specificity and interactions with peptide-MHC, but structural information has long been elusive. In this study, we present structures for the well-studied 2B4 TCR, as well as a naturally occurring variant of the 5c.c7 TCR, 226, which is cross-reactive with more than half of possible substitutions at all three TCR-sensitive residues on the peptide Ag. These structures alone and in complex with peptide-MHC ligands allow us to reassess many prior mutagenesis results. In addition, the structure of 226 bound to one peptide variant, p5E, shows major changes in the CDR3 contacts compared with wild-type, yet the TCR V-region contacts with MHC are conserved. These and other data illustrate the ability of TCRs to accommodate large variations in CDR3 structure and peptide contacts within the constraints of highly conserved TCR-MHC interactions.


    Organizational Affiliation

    Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
H-2 class II histocompatibility antigen, E-K alpha chain
A
193Mus musculusMutation(s): 0 
Find proteins for P04224 (Mus musculus)
Go to UniProtKB:  P04224
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MHC class II E-beta-k
B
202Mus musculusMutation(s): 0 
Gene Names: H2-Eb1
Find proteins for P04230 (Mus musculus)
Go to UniProtKB:  P04230
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
T-cell receptor alpha chain C region
C
207Homo sapiensMutation(s): 0 
Gene Names: TRAC (TCRA)
Find proteins for P01848 (Homo sapiens)
Go to UniProtKB:  P01848
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
2B4 beta chain
D
270N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
MCC peptide
P
13Manduca sextaMutation(s): 0 
Find proteins for P00039 (Manduca sexta)
Go to UniProtKB:  P00039
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FUC
Query on FUC

Download SDF File 
Download CCD File 
B, C
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
C
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
B, C, D
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.221 
  • Space Group: F 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 146.749α = 90.00
b = 167.178β = 90.00
c = 259.489γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-04-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-08-10
    Type: Database references