6WL4

preTCRbeta-pMHC complex crystal structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Pre-T cell receptors topologically sample self-ligands during thymocyte beta-selection.

Li, X.Mizsei, R.Tan, K.Mallis, R.J.Duke-Cohan, J.S.Akitsu, A.Tetteh, P.W.Dubey, A.Hwang, W.Wagner, G.Lang, M.J.Arthanari, H.Wang, J.H.Reinherz, E.L.

(2021) Science 371: 181-185

  • DOI: https://doi.org/10.1126/science.abe0918
  • Primary Citation of Related Structures:  
    6WL2, 6WL3, 6WL4, 7JI2

  • PubMed Abstract: 

    Self-discrimination, a critical but ill-defined molecular process programmed during thymocyte development, requires myriad pre-T cell receptors (preTCRs) and αβTCRs. Using x-ray crystallography, we show how a preTCR applies the concave β-sheet surface of its single variable domain (Vβ) to "horizontally" grab the protruding MHC α2-helix. By contrast, αβTCRs purpose all six complementarity-determining region (CDR) loops of their paired VαVβ module to recognize peptides bound to major histocompatibility complex molecules (pMHCs) in "vertical" head-to-head binding. The preTCR topological fit ensures that CDR3β reaches the peptide's featured C-terminal segment for pMHC sampling, establishing the subsequent αβTCR canonical docking mode. "Horizontal" docking precludes germline CDR1β- and CDR2β-MHC binding to broaden β-chain repertoire diversification before αβTCR-mediated selection refinement. Thus, one subunit successively attunes the recognition logic of related multicomponent receptors.


  • Organizational Affiliation

    Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, USA. jwang@crystal.harvard.edu ellis_reinherz@dfci.harvard.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
H-2 class I histocompatibility antigen, K-B alpha chain
A, D, G
185Mus musculusMutation(s): 2 
Gene Names: H2-K1H2-K
UniProt
Find proteins for P01901 (Mus musculus)
Explore P01901 
Go to UniProtKB:  P01901
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01901
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ARG-GLY-TYR-VAL-TYR-GLN-GLY-LEU
B, E, H
8Vesicular stomatitis virusMutation(s): 0 
UniProt
Find proteins for P03521 (Vesicular stomatitis Indiana virus (strain San Juan))
Explore P03521 
Go to UniProtKB:  P03521
Entity Groups  
UniProt GroupP03521
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
N15 preTCR beta
C, F, I
239Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.546α = 90
b = 110.546β = 90
c = 316.917γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
PDB_EXTRACTdata extraction
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesR01AI136301

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-23
    Type: Initial release
  • Version 1.1: 2020-12-30
    Changes: Database references
  • Version 1.2: 2021-01-20
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Database references, Refinement description