6BMH

Crystal structure of MHC-I like protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 

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Ligand Structure Quality Assessment 


This is version 3.1 of the entry. See complete history


Literature

Differing roles of CD1d2 and CD1d1 proteins in type I natural killer T cell development and function.

Sundararaj, S.Zhang, J.Krovi, S.H.Bedel, R.Tuttle, K.D.Veerapen, N.Besra, G.S.Khandokar, Y.Praveena, T.Le Nours, J.Matsuda, J.L.Rossjohn, J.Gapin, L.

(2018) Proc Natl Acad Sci U S A 115: E1204-E1213

  • DOI: https://doi.org/10.1073/pnas.1716669115
  • Primary Citation of Related Structures:  
    6BMH, 6BMK

  • PubMed Abstract: 

    MHC class I-like CD1 molecules have evolved to present lipid-based antigens to T cells. Differences in the antigen-binding clefts of the CD1 family members determine the conformation and size of the lipids that are presented, although the factors that shape CD1 diversity remain unclear. In mice, two homologous genes, CD1D1 and CD1D2, encode the CD1d protein, which is essential to the development and function of natural killer T (NKT) cells. However, it remains unclear whether both CD1d isoforms are equivalent in their antigen presentation capacity and functions. Here, we report that CD1d2 molecules are expressed in the thymus of some mouse strains, where they select functional type I NKT cells. Intriguingly, the T cell antigen receptor repertoire and phenotype of CD1d2-selected type I NKT cells in CD1D1 -/- mice differed from CD1d1-selected type I NKT cells. The structures of CD1d2 in complex with endogenous lipids and a truncated acyl-chain analog of α-galactosylceramide revealed that its A'-pocket was restricted in size compared with CD1d1. Accordingly, CD1d2 molecules could not present glycolipid antigens with long acyl chains efficiently, favoring the presentation of short acyl chain antigens. These results indicate that the two CD1d molecules present different sets of self-antigen(s) in the mouse thymus, thereby impacting the development of invariant NKT cells.


  • Organizational Affiliation

    Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Antigen-presenting glycoprotein CD1d2
A, C, E, G
276Mus musculusMutation(s): 0 
Gene Names: Cd1d2Cd1.2
UniProt
Find proteins for P11610 (Mus musculus)
Explore P11610 
Go to UniProtKB:  P11610
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11610
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, D, F, H
99Mus musculusMutation(s): 0 
Gene Names: B2m
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus)
Explore P01887 
Go to UniProtKB:  P01887
IMPC:  MGI:88127
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01887
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
I, J, K, L
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F61
Query on F61

Download Ideal Coordinates CCD File 
M [auth A],
O [auth C],
Q [auth E],
S [auth G]
N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]undecanamide
C35 H69 N O9
XAGHGLSSJDVTMX-NOUVZJLJSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
N [auth A],
P [auth C],
R [auth E],
T [auth G],
U [auth G]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.955α = 90
b = 74.229β = 102.94
c = 117.594γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-31
    Type: Initial release
  • Version 1.1: 2018-02-21
    Changes: Database references
  • Version 2.0: 2018-03-07
    Changes: Advisory, Atomic model, Derived calculations, Non-polymer description, Structure summary
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.1: 2023-10-04
    Changes: Advisory, Data collection, Database references, Refinement description, Structure summary