8SGB | pdb_00008sgb

Crystal Structure of CD1d-lipid complexed with Beta-2-Microglobulin, TCR Alpha-Chain and TCR Beta-Chain

• PDB DOI: https://doi.org/10.2210/pdb8SGB/pdb

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


• Deposited: 2023-04-12 Released: 2024-04-24 
• Deposition Author(s): Chan Yew Poa, K.T.O., Le Nours, J., Rossjohn, J.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.249 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Models: experimental

Literature

Semi-invariant human type II Natural Killer T cells recognise CD1d independently of bound lipids.

Chan Yew Poa, K.T.O., Le Nours, J., Rossjohn, J., Godfrey, D.G., Almeida, C.D.S., Pellicci, D.G., Moody, B.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 104.08 kDa 
• Atom Count: 6,439 
• Modeled Residue Count: 816 
• Deposited Residue Count: 897 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen-presenting glycoprotein CD1d	A	347	Homo sapiens	Mutation(s): 0  Gene Names: CD1D
UniProt & NIH Common Fund Data Resources
Find proteins for P15813 (Homo sapiens) Explore P15813  Go to UniProtKB:  P15813
PHAROS:  P15813 GTEx:  ENSG00000158473
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: P15813-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	100	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
Natural Killer T cell receptor TRAV26A-2 alpha chain	C	207	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Natural Killer T cell receptor TRBV19 beta chain	D	243	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FO4 (Subject of Investigation/LOI)	H [auth A]	sphingomyelin C47 H94 N2 O6 P NHYQHBPEJLFFSO-QYKFWSDSSA-O
NAG	F [auth A], G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
NA	I [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.249 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.785	α = 90
b = 136.785	β = 90
c = 69.797	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-04-24 
Deposition Author(s): Chan Yew Poa, K.T.O., Le Nours, J., Rossjohn, J.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	--

Revision History  

• Version 1.0: 2024-04-24
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Structure summary