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 2-mer - AB 

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

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

Biological Assembly 3  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 182312.03 
• Atom Count: 12215 
• Residue Count: 1524 
• Unique protein chains: 2

3L9R

Crystal structure of bovine CD1b3 with endogenously bound ligands

• DOI: 10.2210/pdb3L9R/pdb

• Classification: Immune Response
• Organism(s): Bos taurus
• Expression System: Spodoptera frugiperda


• Deposited: 2010-01-05 Released: 2010-06-16 
• Deposition Author(s): Zajonc, D.M., Girardi, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.248 
• R-Value Work: 0.201 

Literature

Crystal structure of bovine CD1b3 with endogenously bound ligands.

Girardi, E., Wang, J., Mac, T.T., Versluis, C., Bhowruth, V., Besra, G., Heck, A.J., Van Rhijn, I., Zajonc, D.M.

(2010) J.Immunol. 185: 376-386

• PubMed: 20519644 
• DOI: 10.4049/jimmunol.1000042


• PubMed Abstract: 
  

The CD1 family of Ag-presenting molecules is able to display lipids to T cells by binding them within a hydrophobic groove connected to the protein surface. In particular, the CD1b isotype is capable of binding ligands with greatly varying alkyl chain lengths through a complex network of interconnected hydrophobic pockets. Interestingly, mycobacterial lipids such as glucose monomycolate exclusively bind to CD1b. We determined the crystal structure of one of the three expressed bovine CD1b proteins, CD1b3, in complex with endogenous ligands, identified by mass spectrometry as a mixture of phosphatidylcholine and phosphatidylethanolamine, and analyzed the ability of the protein to bind glycolipids in vitro. The structure reveals a complex binding groove architecture, similar to the human ortholog but with consequential differences. Intriguingly, in bovine CD1b3 only the A', C' and F' pockets are present, whereas the T' pocket previously described in human CD1b is closed. This different pocket conformation could affect the ability of boCD1b3 to recognize lipids with long acyl chains such as glucose monomycolate. However, even in the absence of a T' tunnel, bovine CD1b3 is able to bind mycolates from Rhodococcus ruber in vitro.

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Organizational Affiliation: 

Division of Cell Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
CD1b3	A, C, E, G	283	Bos taurus	Mutation(s): 0  Gene Names: CD1B3 (CD1B)
Find proteins for Q1L1H6 (Bos taurus) Go to UniProtKB:  Q1L1H6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Beta-2-microglobulin	B, D, F, H	98	Bos taurus	Mutation(s): 0  Gene Names: B2M
Find proteins for P01888 (Bos taurus) Go to Gene View: B2M Go to UniProtKB:  P01888

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
L9Q	C, G	(1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate 1-stearoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine C41 H80 N O8 P JQKOHRZNEOQNJE-VYCVAHKRSA-N
L9R	A, E	(2S)-3-(octadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate 1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine C44 H86 N O8 P ATHVAWFAEPLPPQ-FLHXZNPISA-N
CL	C, G	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
GOL	A, C, E, G	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MAN	A	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
FUC	A, C, E, G	ALPHA-L-FUCOSE C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
BMA	A, C, E, G	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
NAG	A, C, E, G	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.248 
• R-Value Work: 0.201 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 137.533	α = 90.00
b = 139.975	β = 90.00
c = 111.953	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
MOLREP	phasing
HKL-2000	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-01-05 
• Released Date: 2010-06-16 
• Deposition Author(s): Zajonc, D.M., Girardi, E.

Revision History 

• Version 1.0: 2010-06-16
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance