5L2K | pdb_00005l2k

Crystal structure of GEM42 TCR-CD1b-GMM complex

• PDB DOI: https://doi.org/10.2210/pdb5L2K/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens, Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-08-02 Released: 2016-11-16 
• Deposition Author(s): Gras, S., Shahine, A., Le Nours, J., Rossjohn, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.239 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.218 (Depositor) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Models: experimental

Literature

T cell receptor recognition of CD1b presenting a mycobacterial glycolipid.

Gras, S., Van Rhijn, I., Shahine, A., Cheng, T.Y., Bhati, M., Tan, L.L., Halim, H., Tuttle, K.D., Gapin, L., Le Nours, J., Moody, D.B., Rossjohn, J.

(2016) Nat Commun 7: 13257-13257

• PubMed: 27807341 
• DOI: https://doi.org/10.1038/ncomms13257
• Primary Citation Related Structures: 
  5L2J, 5L2K


• PubMed Abstract: 
  

  CD1 proteins present microbial lipids to T cells. Germline-encoded mycolyl lipid-reactive (GEM) T cells with conserved αβ T cell receptors (TCRs) recognize CD1b presenting mycobacterial mycolates. As the molecular basis underpinning TCR recognition of CD1b remains unknown, here we determine the structure of a GEM TCR bound to CD1b presenting glucose-6-O-monomycolate (GMM). The GEM TCR docks centrally above CD1b, whereby the conserved TCR α-chain extensively contacts CD1b and GMM. Through mutagenesis and study of T cells from tuberculosis patients, we identify a consensus CD1b footprint of TCRs present among GEM T cells. Using both the TCR α- and β-chains as tweezers to surround and grip the glucose moiety of GMM, GEM TCRs create a highly specific mechanism for recognizing this mycobacterial glycolipid.

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Organizational Affiliation: 
• Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.
Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia.
Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus and National Jewish Health, Aurora, Colorado, USA.
Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Hetero 16-mer - A4B4C4D4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 97.84 kDa 
• Atom Count: 6,497 
• Modeled Residue Count: 801 
• Deposited Residue Count: 845 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell surface glycoprotein CD1b	A	300	Homo sapiens	Mutation(s): 1  Gene Names: CD1B
UniProt & NIH Common Fund Data Resources
Find proteins for P29016 (Homo sapiens) Explore P29016  Go to UniProtKB:  P29016
PHAROS:  P29016 GTEx:  ENSG00000158485
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: P29016-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	98	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
PHAROS:  P61769 GTEx:  ENSG00000166710

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
GEM42 TCR alpha chain	C [auth D]	204	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
GEM42 TCR beta chain	D [auth E]	243	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
70E	U [auth E]	6-O-[(2R,3R)-3-hydroxy-2-tetradecyldocosanoyl]-alpha-L-idopyranose C42 H82 O8 YOCZDGRJDQLKHW-GWLFWXKWSA-N
6UL	O [auth A]	TETRACOSYL PALMITATE C40 H80 O2 KKTAIMZGSAQXRE-UHFFFAOYSA-N
NAG	E [auth A], F [auth A], G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CS	R [auth D]	CESIUM ION Cs NCMHKCKGHRPLCM-UHFFFAOYSA-N
SO4	H [auth A], I [auth A], J [auth A], Q [auth D], S [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	K [auth A], L [auth A], M [auth A], P [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	N [auth A], T [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.239 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.218 (Depositor) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.998	α = 90
b = 174.998	β = 90
c = 170.869	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-16 
Deposition Author(s): Gras, S., Shahine, A., Le Nours, J., Rossjohn, J.

Revision History  

• Version 1.0: 2016-11-16
  Type: Initial release
  
• Version 1.1: 2016-12-07
  Changes: Other
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-10-04
  Changes: Advisory, Data collection, Database references, Refinement description, Structure summary
• Version 1.4: 2024-10-09
  Changes: Structure summary