3L9R

Crystal structure of bovine CD1b3 with endogenously bound ligands


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • 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 chai ...

    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.


    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
MoleculeChainsSequence LengthOrganismDetails
CD1b3
A, C, E, G
283Bos taurusMutation(s): 0 
Gene Names: CD1B3 (CD1B)
Find proteins for Q1L1H6 (Bos taurus)
Go to UniProtKB:  Q1L1H6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B, D, F, H
98Bos taurusMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L9Q
Query on L9Q

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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
 Ligand Interaction
L9R
Query on L9R

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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
 Ligand Interaction
CL
Query on CL

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C, G
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A, C, E, G
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

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A, C, E, G
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
A, C, E, G
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

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A, C, E, G
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
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 = 137.533α = 90.00
b = 139.975β = 90.00
c = 111.953γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
MOLREPphasing
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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