1NFD

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

• PDB DOI:  https://doi.org/10.2210/pdb1NFD/pdb

• Classification: COMPLEX (IMMUNORECEPTOR/IMMUNOGLOBULIN)
• Organism(s): Mus musculus
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 1997-08-04 Released: 1998-01-28 
• Deposition Author(s): Wang, J.-H., Lim, K., Smolyar, A., Teng, M.-K., Sacchittini, J., Reinherz, E.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.309 
• R-Value Work: 0.243 
• R-Value Observed: 0.243 

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

• PubMed: 9427737 
• DOI: https://doi.org/10.1093/emboj/17.1.10
• Primary Citation of Related Structures:  
  1NFD


• 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 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.

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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

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 2 assigned by authors and generated by PQS (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B2C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A3B2C1 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 197.64 kDa 
• Atom Count: 13,884 
• Modelled Residue Count: 1,752 
• Deposited Residue Count: 1,752 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N15 ALPHA-BETA T-CELL RECEPTOR	A, C	203	Mus musculus	Mutation(s): 0  Gene Names: N15 T-CELL RECEPTOR, Tcra
UniProt
Find proteins for P01849 (Mus musculus) Explore P01849  Go to UniProtKB:  P01849

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
N15 ALPHA-BETA T-CELL RECEPTOR	B, D	239	Mus musculus	Mutation(s): 0  Gene Names: N15 T-CELL RECEPTOR
UniProt
Find proteins for P01852 (Mus musculus) Explore P01852  Go to UniProtKB:  P01852

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
H57 FAB	E, G	212	Mus musculus	Mutation(s): 0  Gene Names: N15 T-CELL RECEPTOR

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
H57 FAB	F, H	222	Mus musculus	Mutation(s): 0  Gene Names: N15 T-CELL RECEPTOR

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	I [auth A], J [auth A], K [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth C], Q [auth C], R [auth C], S [auth D], T [auth D], U [auth D], V [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.309 
• R-Value Work: 0.243 
• R-Value Observed: 0.243 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.74	α = 90
b = 122.3	β = 107.95
c = 115.84	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-01-28 
Deposition Author(s): Wang, J.-H., Lim, K., Smolyar, A., Teng, M.-K., Sacchittini, J., Reinherz, E.L.

Revision History  

• Version 1.0: 1998-01-28
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-07-05
  Changes: Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-08-09
  Changes: Database references, Refinement description, Structure summary