5IW1 | pdb_00005iw1

Crystal Structure of B4.2.3 T-Cell Receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.268 (Depositor), 0.279 (DCC) 
  • R-Value Work: 
    0.240 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 
    0.243 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

An allosteric site in the T-cell receptor C beta domain plays a critical signalling role.

Natarajan, K.McShan, A.C.Jiang, J.Kumirov, V.K.Wang, R.Zhao, H.Schuck, P.Tilahun, M.E.Boyd, L.F.Ying, J.Bax, A.Margulies, D.H.Sgourakis, N.G.

(2017) Nat Commun 8: 15260-15260

  • DOI: https://doi.org/10.1038/ncomms15260
  • Primary Citation Related Structures: 
    5IVX, 5IW1

  • PubMed Abstract: 

    The molecular mechanism through which the interaction of a clonotypic αβ T-cell receptor (TCR) with a peptide-loaded major histocompatibility complex (p/MHC) leads to T-cell activation is not yet fully understood. Here we exploit a high-affinity TCR (B4.2.3) to examine the structural changes that accompany binding to its p/MHC ligand (P18-I10/H2-D d ). In addition to conformational changes in complementarity-determining regions (CDRs) of the TCR seen in comparison of unliganded and bound X-ray structures, NMR characterization of the TCR β-chain dynamics reveals significant chemical shift effects in sites removed from the MHC-binding site. Remodelling of electrostatic interactions near the Cβ H3 helix at the membrane-proximal face of the TCR, a region implicated in interactions with the CD3 co-receptor, suggests a possible role for an allosteric mechanism in TCR signalling. The contribution of these TCR residues to signal transduction is supported by mutagenesis and T-cell functional assays.


  • Organizational Affiliation
    • Molecular Biology Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.

Macromolecule Content 

  • Total Structure Weight: 145.7 kDa 
  • Atom Count: 10,062 
  • Modeled Residue Count: 1,266 
  • Deposited Residue Count: 1,287 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
T-CELL RECEPTOR ALPHA CHAIN
A, C, E
194Mus musculusMutation(s): 0 
Gene Names: TCRAV2S6J38
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
T-CELL RECEPTOR BETA CHAIN
B, D, F
235Mus musculusMutation(s): 0 
Gene Names: TCRAV2S6J38

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.268 (Depositor), 0.279 (DCC) 
  • R-Value Work:  0.240 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 0.243 (Depositor) 
Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.112α = 90
b = 96.112β = 90
c = 167.578γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2017-06-21
    Changes: Database references
  • Version 1.2: 2023-09-27
    Changes: Advisory, Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary