1NFD

AN ALPHA-BETA T CELL RECEPTOR (TCR) HETERODIMER IN COMPLEX WITH AN ANTI-TCR FAB FRAGMENT DERIVED FROM A MITOGENIC ANTIBODY

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Atomic structure of an alphabeta T cell receptor (TCR) heterodimer in complex with an anti-TCR fab fragment derived from a mitogenic antibody.

Wang, J., Lim, K., Smolyar, A., Teng, M., Liu, J., Tse, A.G., Liu, J., Hussey, R.E., Chishti, Y., Thomson, C.T., Sweet, R.M., Nathenson, S.G., Chang, H.C., Sacchettini, J.C., Reinherz, E.L.

(1998) EMBO J. 17: 10-26

  • DOI: 10.1093/emboj/17.1.10

  • PubMed Abstract: 

    • Each T cell receptor (TCR) recognizes a peptide antigen bound to a major histocompatibility complex (MHC) molecule via a clonotypic alphabeta heterodimeric structure (Ti) non-covalently associated with the monomorphic CD3 signaling components. A crys ...

    Each T cell receptor (TCR) recognizes a peptide antigen bound to a major histocompatibility complex (MHC) molecule via a clonotypic alphabeta heterodimeric structure (Ti) non-covalently associated with the monomorphic CD3 signaling components. A crystal structure of an alphabeta TCR-anti-TCR Fab complex shows an Fab fragment derived from the H57 monoclonal antibody (mAb), interacting with the elongated FG loop of the Cbeta domain, situated beneath the Vbeta domain. This loop, along with the partially exposed ABED beta sheet of Cbeta, and glycans attached to both Cbeta and Calpha domains, forms a cavity of sufficient size to accommodate a single non-glycosylated Ig domain such as the CD3epsilon ectodomain. That this asymmetrically localized site is embedded within the rigid constant domain module has implications for the mechanism of signal transduction in both TCR and pre-TCR complexes. Furthermore, quaternary structures of TCRs vary significantly even when they bind the same MHC molecule, as manifested by a unique twisting of the V module relative to the C module.

    Related Citations: 
    • Crystallization of a Deglycosylated T Cell Receptor (Tcr) Complexed with an Anti-Tcr Fab Fragment
      Liu, J.,Tse, A.G.,Chang, H.C.,Liu, J.H.,Wang, J.,Hussey, R.E.,Chishti, Y.,Rheinhold, B.,Spoerl, R.,Nathenson, S.G.,Sacchettini, J.C.,Reinherz, E.L.
      (1996) J.Biol.Chem. 271: 33639

    Organizational Affiliation: 

    Laboratory of Immunobiology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N15 ALPHA-BETA T-CELL RECEPTOR
A, C
203Mus musculusMutation(s): 0 
Gene Names: Tcra
Find proteins for P01849 (Mus musculus)
Go to UniProtKB:  P01849
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
N15 ALPHA-BETA T-CELL RECEPTOR
B, D
239Mus musculusMutation(s): 0 
Find proteins for P01852 (Mus musculus)
Go to UniProtKB:  P01852
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
H57 FAB
E, G
212N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
H57 FAB
F, H
222N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDG
Query on NDG
Download SDF File 
Download CCD File 
B, C
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.243 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 74.740α = 90.00
b = 122.300β = 107.95
c = 115.840γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-01-28
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-07-05
    Type: Other