5IVX

Crystal Structure of B4.2.3 T-Cell Receptor and H2-Dd P18-I10 Complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

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This is version 1.1 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: 10.1038/ncomms15260
  • Primary Citation of 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 ...

    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: 

    Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
H-2 class I histocompatibility antigen, D-D alpha chainA277Mus musculusMutation(s): 0 
Gene Names: H2-D1
UniProt
Find proteins for P01900 (Mus musculus)
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UniProt GroupP01900
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB100Mus musculusMutation(s): 0 
Gene Names: B2m
UniProt & NIH Common Fund Data Resources
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IMPC:  MGI:88127
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
T-CELL RECEPTOR ALPHA CHAINC [auth E]194Mus musculusMutation(s): 0 
Gene Names: TCRAV2S6J38
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
T-CELL RECEPTOR BETA CHAIND [auth F]234Mus musculusMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
P18-I10E [auth P]10Homo sapiensMutation(s): 0 
UniProt
Find proteins for P04578 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
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Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 210.107α = 90
b = 51.316β = 97.14
c = 93.741γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata 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