This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
2fik
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 2fik |SIZE=350|CAPTION= <scene name='initialview01'>2fik</scene>, resolution 1.80Å | |PDB= 2fik |SIZE=350|CAPTION= <scene name='initialview01'>2fik</scene>, resolution 1.80Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=GSL:(2S,3R)-3-HYDROXY-2-(TETRADECANOYLAMINO)OCTADECYL+ALPHA-D-GALACTOPYRANOSIDURONIC+ACID'>GSL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= Cd1d1, Cd1.1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus]), beta-2-microglobulin ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus]) | |GENE= Cd1d1, Cd1.1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus]), beta-2-microglobulin ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1z5l|1Z5L]], [[2akr|2AKR]], [[1zhn|1ZHN]], [[1zt4|1ZT4]], [[1cd1|1CD1]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2fik FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fik OCA], [http://www.ebi.ac.uk/pdbsum/2fik PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2fik RCSB]</span> | ||
}} | }} | ||
| Line 24: | Line 27: | ||
[[Category: Wu, D.]] | [[Category: Wu, D.]] | ||
[[Category: Zajonc, D M.]] | [[Category: Zajonc, D M.]] | ||
| - | [[Category: GSL]] | ||
| - | [[Category: NAG]] | ||
| - | [[Category: PLM]] | ||
[[Category: bacterial antigen]] | [[Category: bacterial antigen]] | ||
[[Category: cd1d]] | [[Category: cd1d]] | ||
| Line 34: | Line 34: | ||
[[Category: tcr]] | [[Category: tcr]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:03:13 2008'' |
Revision as of 00:03, 31 March 2008
| |||||||
| , resolution 1.80Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Gene: | Cd1d1, Cd1.1 (Mus musculus), beta-2-microglobulin (Mus musculus) | ||||||
| Related: | 1Z5L, 2AKR, 1ZHN, 1ZT4, 1CD1
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Structure of a microbial glycosphingolipid bound to mouse CD1d
Overview
Natural killer T (NKT) cells provide an innate-type immune response upon T cell receptor interaction with CD1d-presented antigens. We demonstrate through equilibrium tetramer binding and antigen presentation assays with Valpha14i-positive NKT cell hybridomas that the Sphingomonas glycolipid alpha-galacturonosyl ceramide (GalA-GSL) is a NKT cell agonist that is significantly weaker than alpha-galactosylceramide (alpha-GalCer), the most potent known NKT agonist. For GalA-GSL, a shorter fatty acyl chain, an absence of the 4-OH on the sphingosine tail and a 6'-COOH group on the galactose moiety account for its observed antigenic potency. We further determined the crystal structure of mCD1d in complex with GalA-GSL at 1.8-A resolution. The overall binding mode of GalA-GSL to mCD1d is similar to that of the short-chain alpha-GalCer ligand PBS-25, but its sphinganine chain is more deeply inserted into the F' pocket due to alternate hydrogen-bonding interactions between the sphinganine 3-OH with Asp-80. Subsequently, a slight lateral shift (>1 A) of the galacturonosyl head group is noted at the CD1 surface compared with the galactose of alpha-GalCer. Because the relatively short C(14) fatty acid of GalA-GSL does not fully occupy the A' pocket, a spacer lipid is found that stabilizes this pocket. The lipid spacer was identified by GC/MS as a mixture of saturated and monounsaturated palmitic acid (C(16)). Comparison of available crystal structures of alpha-anomeric glycosphingolipids now sheds light on the structural basis of their differential antigenic potency and has led to the design and synthesis of NKT cell agonists with enhanced cell-based stimulatory activities compared with alpha-GalCer.
About this Structure
2FIK is a Protein complex structure of sequences from Mus musculus. Full crystallographic information is available from OCA.
Reference
Design of natural killer T cell activators: structure and function of a microbial glycosphingolipid bound to mouse CD1d., Wu D, Zajonc DM, Fujio M, Sullivan BA, Kinjo Y, Kronenberg M, Wilson IA, Wong CH, Proc Natl Acad Sci U S A. 2006 Mar 14;103(11):3972-7. Epub 2006 Mar 6. PMID:16537470
Page seeded by OCA on Mon Mar 31 03:03:13 2008
Categories: Mus musculus | Protein complex | Wu, D. | Zajonc, D M. | Bacterial antigen | Cd1d | Immune system | Mhc-fold | Nkt cell | Tcr
