3ILQ

Structure of mCD1d with bound glycolipid BbGL-2c from Borrelia burgdorferi

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

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Literature

Lipid binding orientation within CD1d affects recognition of Borrelia burgorferi antigens by NKT cells.

Wang, J., Li, Y., Kinjo, Y., Mac, T.T., Gibson, D., Painter, G.F., Kronenberg, M., Zajonc, D.M.

(2010) Proc Natl Acad Sci U S A 107: 1535-1540

  • DOI: 10.1073/pnas.0909479107
  • Primary Citation of Related Structures:  
    3ILP, 3ILQ

  • PubMed Abstract: 

    • Invariant natural killer T cells (iNKT cells) respond to CD1d-presented glycolipids from Borrelia burgdorferi, the causative agent of Lyme disease. Although mouse and human iNKT cells respond to different antigens based on subtle differences in their fatty acids, the mechanism by which fatty acid structure determines antigenic potency is not well understood ...

    Invariant natural killer T cells (iNKT cells) respond to CD1d-presented glycolipids from Borrelia burgdorferi, the causative agent of Lyme disease. Although mouse and human iNKT cells respond to different antigens based on subtle differences in their fatty acids, the mechanism by which fatty acid structure determines antigenic potency is not well understood. Here we show that the mouse and human CD1d present glycolipids having different fatty acids, based in part upon a difference at a single amino acid position that is involved in positioning the sugar epitope. CD1d also can bind nonantigenic lipids, however, but unexpectedly, mouse CD1d orients the two aliphatic chains of a nonantigenic lipid rotated 180 degrees, causing a dramatic repositioning of the exposed sugar. Therefore, our data reveal the biochemical basis for the high degree of antigenic specificity of iNKT cells for certain fatty acids, and they suggest how microbes could alter fatty acid biosynthesis as an immune evasion mechanism.

    Organizational Affiliation: 

    Division of Cell Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD1d1A [auth C]285Mus musculusMutation(s): 0 
Gene Names: Cd1.1, CD1d, Cd1d1
UniProt
Find proteins for P11609 (Mus musculus)
Explore P11609 
Go to UniProtKB:  P11609
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2 microglobulinB [auth D]99Mus musculusMutation(s): 0 
Gene Names: B2m, beta 2 microblobulin, mCG_11606, RP23-34E24.5-001
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus)
Explore P01887 
Go to UniProtKB:  P01887
IMPC:  MGI:88127
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth A]2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1O2 (Subject of Investigation/LOI)
Query on 1O2
Download Ideal Coordinates CCD File 
F [auth C](2S)-3-(alpha-D-galactopyranosyloxy)-2-(hexadecanoyloxy)propyl (9Z)-octadec-9-enoate
C43 H80 O10
JBZBYHKCRFIXBI-BNOJPGAFSA-N		 Ligand Interaction
NAG (Subject of Investigation/LOI)
Query on NAG
Download Ideal Coordinates CCD File 
D [auth C], E [auth C]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
1O2 PDBBind:  3ILQ Kd: 6200 (nM) from 1 assay(s)
Binding MOAD:  3ILQ Kd: 6200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.706α = 90
b = 97.791β = 106.94
c = 55.421γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2009-08-07 
  • Released Date: 2010-01-26 
    • Deposition Author(s): Zajonc, D.M.

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary