7K0Z | pdb_00007k0z

Marsupial T cell receptor Spl_157

• PDB DOI: https://doi.org/10.2210/pdb7K0Z/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Monodelphis domestica
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2020-09-06 Released: 2021-03-24 
• Deposition Author(s): Wegrecki, M., Kannan Sivaraman, K., Le Nours, J., Rossjohn, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.285 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.257 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.259 (Depositor) 

Starting Model: other

Literature

The molecular assembly of the marsupial gamma mu T cell receptor defines a third T cell lineage.

Morrissey, K.A., Wegrecki, M., Praveena, T., Hansen, V.L., Bu, L., Sivaraman, K.K., Darko, S., Douek, D.C., Rossjohn, J., Miller, R.D., Le Nours, J.

(2021) Science 371: 1383-1388

• PubMed: 33766885 
• DOI: https://doi.org/10.1126/science.abe7070
• Primary Citation Related Structures: 
  7K0X, 7K0Z, 7L15


• PubMed Abstract: 
  

  αβ and γδ T cell receptors (TCRs) are highly diverse antigen receptors that define two evolutionarily conserved T cell lineages. We describe a population of γμTCRs found exclusively in non-eutherian mammals that consist of a two-domain (Vγ-Cγ) γ-chain paired to a three-domain (Vμ-Vμj-Cμ) μ-chain. γμTCRs were characterized by restricted diversity in the Vγ and Vμj domains and a highly diverse unpaired Vμ domain. Crystal structures of two distinct γμTCRs revealed the structural basis of the association of the γμTCR heterodimer. The Vμ domain shared the characteristics of a single-domain antibody within which the hypervariable CDR3μ loop suggests a major antigen recognition determinant. We define here the molecular basis underpinning the assembly of a third TCR lineage, the γμTCR.

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Organizational Affiliation: 
• Department of Biology, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM, USA.
Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia.
Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia. [e-mail] [e-mail] [e-mail].
Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK.
Department of Biology, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM, USA. [e-mail] [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 130.64 kDa 
• Atom Count: 7,936 
• Modeled Residue Count: 1,085 
• Deposited Residue Count: 1,170 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor mu chain	A [auth C], C [auth A]	349	Monodelphis domestica	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor gamma chain	B [auth D], D [auth B]	236	Monodelphis domestica	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.285 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.257 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.259 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.328	α = 90
b = 110.722	β = 90
c = 207.798	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-03-24 
Deposition Author(s): Wegrecki, M., Kannan Sivaraman, K., Le Nours, J., Rossjohn, J.

Revision History  

• Version 1.0: 2021-03-24
  Type: Initial release
  
• Version 1.1: 2021-04-14
  Changes: Database references
• Version 1.2: 2024-04-03
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary