Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis, gel filtration

Macromolecule Content

• Total Structure Weight: 99216.44 
• Atom Count: 6545 
• Residue Count: 852 
• Unique protein chains: 4

5WKI

Crystal structure of PG90 TCR-CD1b-PG complex

• DOI: 10.2210/pdb5WKI/pdb

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


• Deposited: 2017-07-25 Released: 2017-11-01 
• Deposition Author(s): Shahine, A., Gras, S., Rossjohn, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.252 
• R-Value Work: 0.212 

Literature

A molecular basis of human T cell receptor autoreactivity toward self-phospholipids.

Shahine, A., Van Rhijn, I., Cheng, T.Y., Iwany, S., Gras, S., Moody, D.B., Rossjohn, J.

(2017) Sci Immunol 2: --

• PubMed: 29054999 
• DOI: 10.1126/sciimmunol.aao1384
• Primary Citation of Related Structures:  
  5WL1, 5WKG, 5WKE, 5WJO


• PubMed Abstract: 
  

Human T cell autoreactivity toward lipid antigens presented by CD1 proteins can manifest in numerous diseases, including psoriasis, contact hypersensitivities, and allergies. However, the molecular mechanisms for regulating T cell autoreactivity toward lipid antigens remain unclear. We determined the basis for T cell receptor (TCR) autoreactivity toward CD1b bound to self-phospholipids. The spectrum of self-antigens captured by CD1b skews toward abundant membrane phospholipids such as phosphatidylcholine and phosphatidylethanolamine. However, TCRs can specifically recognize rare phospholipids, including phosphatidylglycerol (PG). The structure of an autoreactive TCR bound to CD1b-PG shows that discrimination occurs through a marked induced fit movement of PG so that its polar head group fits snugly into the cationic cup of the TCR. Conversely, TCR binding toward ubiquitous self-phospholipids was sterically or electrostatically repelled. Accordingly, we describe a mechanism of TCR autoreactivity toward rare phospholipids and avoidance of autoreactivity to the most abundant self-phospholipids.

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Organizational Affiliation: 

Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
T-cell surface glycoprotein CD1b	A	300	Homo sapiens	Mutation(s): 0  Gene Names: CD1B
Find proteins for P29016 (Homo sapiens) Go to Gene View: CD1B Go to UniProtKB:  P29016

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Beta-2-microglobulin	B	99	Homo sapiens	Mutation(s): 0  Gene Names: B2M
Find proteins for P61769 (Homo sapiens) Go to Gene View: B2M Go to UniProtKB:  P61769

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
T-cell receptor alpha variable 26-1,TRA@ protein	D	204	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
PG90 TCR beta chain	E	249	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NA	D, E	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
ACT	E	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	E	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
CUY	A	tetracosyl octadecanoate C42 H84 O2 JKKQRJTZBKHHOI-UHFFFAOYSA-N
FUC	A	ALPHA-L-FUCOSE C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
EDO	A, B, D	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
D3D	D	(19S,22R,25R)-22,25,26-trihydroxy-16,22-dioxo-17,21,23-trioxa-22lambda~5~-phosphahexacosan-19-yl (9E)-octadec-9-enoate C40 H77 O10 P PAZGBAOHGQRCBP-UCZVXENKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.252 
• R-Value Work: 0.212 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 152.010	α = 90.00
b = 82.970	β = 94.88
c = 90.160	γ = 90.00

Software Package:

Software Name	Purpose
Aimless	data scaling
iMOSFLM	data reduction
PHASER	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-07-25 
• Released Date: 2017-11-01 
• Deposition Author(s): Shahine, A., Gras, S., Rossjohn, J.

Revision History 

• Version 1.0: 2017-11-01
  Type: Initial release