6WL2 | pdb_00006wl2

preTCRbeta-pMHC complex crystal structure

• PDB DOI: https://doi.org/10.2210/pdb6WL2/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Vesicular stomatitis virus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-04-18 Released: 2020-12-23 
• Deposition Author(s): Li, X., Mallis, R.J., Mizsei, R., Tan, K., Reinherz, E.L., Wang, J.
• Funding Organization(s): National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.270 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Models: experimental

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

• PubMed: 33335016 
• DOI: https://doi.org/10.1126/science.abe0918
• Primary Citation 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.

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Organizational Affiliation: 
• Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, USA. [e-mail] [e-mail].
Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
Department of Medicine, Harvard Medical School, Boston, MA, USA.
Structural Biology Center, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL, USA.
Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, USA.
Department of Dermatology, Harvard Medical School, Boston, MA, USA.
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA.
Department of Materials Science & Engineering, Texas A&M University, College Station, TX, USA.
Department of Physics & Astronomy, Texas A&M University, College Station, TX, USA.
School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Republic of Korea.
Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA.
Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA.
Department of Pediatrics, Harvard Medical School, Boston, MA, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: cross-linking

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 149.18 kDa 
• Atom Count: 10,279 
• Modeled Residue Count: 1,265 
• Deposited Residue Count: 1,296 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class I histocompatibility antigen, K-B alpha chain	A, D, G	185	Mus musculus	Mutation(s): 2  Gene Names: H2-K1, H2-K
UniProt
Find proteins for P01901 (Mus musculus) Explore P01901  Go to UniProtKB:  P01901

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ARG-GLY-TYR-VAL-TYR-GLN-GLY-LEU	B, E, H	8	Vesicular stomatitis virus	Mutation(s): 0
UniProt
Find proteins for P03521 (Vesicular stomatitis Indiana virus (strain San Juan)) Explore P03521  Go to UniProtKB:  P03521

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
N15 preTCR beta	C, F, I	239	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.270 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.897	α = 90
b = 108.897	β = 90
c = 316.173	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
PDB_EXTRACT	data extraction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-12-23 
Deposition Author(s): Li, X., Mallis, R.J., Mizsei, R., Tan, K., Reinherz, E.L., Wang, J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)	United States	R01AI136301

Revision History  

• 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
• Version 1.4: 2024-10-30
  Changes: Structure summary