6BNL

Crystal structure of TCR-MHC-like molecule


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report



Literature

Dual Modifications of alpha-Galactosylceramide Synergize to Promote Activation of Human Invariant Natural Killer T Cells and Stimulate Anti-tumor Immunity.

Chennamadhavuni, D.Saavedra-Avila, N.A.Carreno, L.J.Guberman-Pfeffer, M.J.Arora, P.Yongqing, T.Koay, H.F.Godfrey, D.I.Keshipeddy, S.Richardson, S.K.Sundararaj, S.Lo, J.H.Wen, X.Gascon, J.A.Yuan, W.Rossjohn, J.Le Nours, J.Porcelli, S.A.Howell, A.R.

(2018) Cell Chem Biol 25: 571

  • DOI: 10.1016/j.chembiol.2018.02.009
  • Primary Citation of Related Structures:  
    6BNK, 6BNL

  • PubMed Abstract: 
  • Glycosylceramides that activate CD1d-restricted invariant natural killer T (iNKT) cells have potential therapeutic applications for augmenting immune responses against cancer and infections. Previous studies using mouse models identified sphinganine ...

    Glycosylceramides that activate CD1d-restricted invariant natural killer T (iNKT) cells have potential therapeutic applications for augmenting immune responses against cancer and infections. Previous studies using mouse models identified sphinganine variants of α-galactosylceramide as promising iNKT cell activators that stimulate cytokine responses with a strongly proinflammatory bias. However, the activities of sphinganine variants in mice have generally not translated well to studies of human iNKT cell responses. Here, we show that strongly proinflammatory and anti-tumor iNKT cell responses were achieved in mice by a variant of α-galactosylceramide that combines a sphinganine base with a hydrocinnamoyl ester on C6″ of the sugar. Importantly, the activities observed with this variant were largely preserved for human iNKT cell responses. Structural and in silico modeling studies provided a mechanistic basis for these findings and suggested basic principles for capturing useful properties of sphinganine analogs of synthetic iNKT cell activators in the design of immunotherapeutic agents.


    Organizational Affiliation

    Department of Chemistry, The University of Connecticut, Storrs, CT 06269-3060, USA. Electronic address: amy.howell@uconn.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Antigen-presenting glycoprotein CD1d1AE302Mus musculusMutation(s): 0 
Gene Names: Cd1d1mCG_3074Cd1.1
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-microglobulinBF99Mus musculusMutation(s): 0 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
Explore P01887 
Go to UniProtKB:  P01887
NIH Common Fund Data Resources
IMPC  MGI:88127
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NKT Valpha14 (MOUSE) - 2C12 TCR - Hybrid mouse variable and human constant domainsCG207Homo sapiensMutation(s): 0 
Gene Names: B2MHDCMA22P
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NKT Vbeta8.2 (MOUSE) - 2C12 TCR - hybrid mouse variable and human constant domainsDH242Mus musculusMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

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Entity ID: 5
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
I, J
2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QWV
Query on QWV

Download Ideal Coordinates CCD File 
A, E
N-[(2S,3R)-3-hydroxy-1-{[6-O-(3-phenylpropanoyl)-alpha-D-galactopyranosyl]oxy}octadecan-2-yl]hexacosanamide
C59 H107 N O9
ROLREGVMOYCGJS-XRHAFTOMSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
A, E
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.666α = 90
b = 150.318β = 96.12
c = 100.144γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-04-04
    Type: Initial release
  • Version 1.1: 2018-04-11
    Changes: Data collection, Database references
  • Version 1.2: 2018-05-30
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary