3OF6 | pdb_00003of6

Human pre-T cell receptor crystal structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.240 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history

Literature

The structural basis for autonomous dimerization of the pre-T-cell antigen receptor

Pang, S.S.Berry, R.Chen, Z.Kjer-Nielsen, L.Perugini, M.A.King, G.F.Wang, C.Chew, S.H.La Gruta, N.L.Williams, N.K.Beddoe, T.Tiganis, T.Cowieson, N.P.Godfrey, D.I.Purcell, A.W.Wilce, M.C.J.McCluskey, J.Rossjohn, J.

(2010) Nature 467: 844-848

  • DOI: https://doi.org/10.1038/nature09448
  • Primary Citation Related Structures: 
    3OF6

  • PubMed Abstract: 

    The pre-T-cell antigen receptor (pre-TCR), expressed by immature thymocytes, has a pivotal role in early T-cell development, including TCR β-selection, survival and proliferation of CD4(-)CD8(-) double-negative thymocytes, and subsequent αβ T-cell lineage differentiation. Whereas αβTCR ligation by the peptide-loaded major histocompatibility complex initiates T-cell signalling, pre-TCR-induced signalling occurs by means of a ligand-independent dimerization event. The pre-TCR comprises an invariant α-chain (pre-Tα) that pairs with any TCR β-chain (TCRβ) following successful TCR β-gene rearrangement. Here we provide the basis of pre-Tα-TCRβ assembly and pre-TCR dimerization. The pre-Tα chain comprised a single immunoglobulin-like domain that is structurally distinct from the constant (C) domain of the TCR α-chain; nevertheless, the mode of association between pre-Tα and TCRβ mirrored that mediated by the Cα-Cβ domains of the αβTCR. The pre-TCR had a propensity to dimerize in solution, and the molecular envelope of the pre-TCR dimer correlated well with the observed head-to-tail pre-TCR dimer. This mode of pre-TCR dimerization enabled the pre-Tα domain to interact with the variable (V) β domain through residues that are highly conserved across the Vβ and joining (J) β gene families, thus mimicking the interactions at the core of the αβTCR's Vα-Vβ interface. Disruption of this pre-Tα-Vβ dimer interface abrogated pre-TCR dimerization in solution and impaired pre-TCR expression on the cell surface. Accordingly, we provide a mechanism of pre-TCR self-association that allows the pre-Tα chain to simultaneously 'sample' the correct folding of both the V and C domains of any TCR β-chain, regardless of its ultimate specificity, which represents a critical checkpoint in T-cell development. This unusual dual-chaperone-like sensing function of pre-Tα represents a unique mechanism in nature whereby developmental quality control regulates the expression and signalling of an integral membrane receptor complex.


  • Organizational Affiliation
    • The Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia.

Macromolecule Content 

  • Total Structure Weight: 126.87 kDa 
  • Atom Count: 8,060 
  • Modeled Residue Count: 1,032 
  • Deposited Residue Count: 1,155 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
T cell receptor beta chain
A, B, C
255Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre T-cell antigen receptor alpha
D, E, F
130Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q6ISU1 (Homo sapiens)
Explore Q6ISU1 
Go to UniProtKB:  Q6ISU1
PHAROS:  Q6ISU1
GTEx:  ENSG00000171611 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6ISU1
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q6ISU1-1
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.240 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.902α = 90
b = 114.902β = 90
c = 183.101γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
PHASESphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2010-10-20 
  • Deposition Author(s): Pang, S.S.

Revision History  (Full details and data files)

  • Version 1.0: 2010-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.4: 2024-10-30
    Changes: Structure summary