2P1Y | pdb_00002p1y

1.B2.D9, a bispecific alpha/beta TCR

• PDB DOI: https://doi.org/10.2210/pdb2P1Y/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-03-06 Released: 2008-02-05 
• Deposition Author(s): McBeth, C., Pizarro, J.C., Strong, R.K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 
  0.254 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

A new twist in TCR diversity revealed by a forbidden alphabeta TCR.

McBeth, C., Seamons, A., Pizarro, J.C., Fleishman, S.J., Baker, D., Kortemme, T., Goverman, J.M., Strong, R.K.

(2008) J Mol Biology 375: 1306-1319

• PubMed: 18155234 
• DOI: https://doi.org/10.1016/j.jmb.2007.11.020
• Primary Citation Related Structures: 
  2P1Y, 2P24


• PubMed Abstract: 
  

  We report crystal structures of a negatively selected T cell receptor (TCR) that recognizes two I-A(u)-restricted myelin basic protein peptides and one of its peptide/major histocompatibility complex (pMHC) ligands. Unusual complementarity-determining region (CDR) structural features revealed by our analyses identify a previously unrecognized mechanism by which the highly variable CDR3 regions define ligand specificity. In addition to the pMHC contact residues contributed by CDR3, the CDR3 residues buried deep within the V alpha/V beta interface exert indirect effects on recognition by influencing the V alpha/V beta interdomain angle. This phenomenon represents an additional mechanism for increasing the potential diversity of the TCR repertoire. Both the direct and indirect effects exerted by CDR residues can impact global TCR/MHC docking. Analysis of the available TCR structures in light of these results highlights the significance of the V alpha/V beta interdomain angle in determining specificity and indicates that TCR/pMHC interface features do not distinguish autoimmune from non-autoimmune class II-restricted TCRs.

---

Organizational Affiliation: 
• Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 105.07 kDa 
• Atom Count: 7,017 
• Modeled Residue Count: 896 
• Deposited Residue Count: 952 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
bispecific alpha/beta TCR	A, B [auth C], C [auth E], D [auth G]	238	Mus musculus	Mutation(s): 0  Gene Names: Valpha2.3/Vbeta8.2
UniProt
Find proteins for Q5R1B3 (Mus musculus) Explore Q5R1B3  Go to UniProtKB:  Q5R1B3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free:  0.254 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.681	α = 90
b = 105.477	β = 116.04
c = 81.531	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-05 
Deposition Author(s): McBeth, C., Pizarro, J.C., Strong, R.K.

Revision History  

• Version 1.0: 2008-02-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary