BMRB Entry 21032

Name: Solution structure of 1,3-Fucosylated chitobiose
Published: 2017-08-30

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR21032

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution structure of 1,3-Fucosylated chitobiose

Deposition date:

2013-01-21

Original release date:

2017-08-30

Authors:

Schubert, Mario; Allain, Frederic; Aeschbacher, Thomas

Citation:

Citation: Aeschbacher, Thomas; Zierke, Mirko; Smiesko, Martin; Collot, Mayeul; Mallet, Jean-Maurice; Ernst, Beat; Allain, Frederic H-T; Schubert, Mario. "A Secondary Structural Element in a Wide Range of Fucosylated Glycoepitopes." Chemistry 23, 11598-11610 (2017).
PubMed: 28654715

Assembly members:

Assembly members:
SUGAR_(3-MER), polymer, 4 residues, 684.69 Da.

Natural source:

Natural source: Common Name: nematode Taxonomy ID: 6239 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Caenorhabditis elegans

Experimental source:

Experimental source: Production method: chemically synthesized

Entity Sequences (FASTA):

Entity Sequences (FASTA):
SUGAR_(3-MER): XXXX

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
- assigned_chem_shift_list

Data type	Count
13C chemical shifts	52
1H chemical shifts	78

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	SUGAR (3-MER)	1

Entities:

Entity 1, SUGAR (3-MER) 4 residues - 684.69 Da.

The trisaccharide contains twice NAG, the terminal NAG (residue 3) is linked to O4 of the proximal NAG. The Proximal NAG (residue 2) is linked via O3 to FUC (residue 4) and via C1 to O6 of 6HH (residue 1).

1

6HH

NAG

FUC

Samples:

sample_1: SUGAR (3-MER) 2.8 mM; D2O 100%

sample_2: SUGAR (3-MER) 2.8 mM; H2O 95%; D2O 5%

sample_conditions_1: pH: 7; temperature: 277 K

sample_conditions_2: pH: 7; temperature: 310 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_2
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_2
2D 1H-13C HSQC long range	sample_1	isotropic	sample_conditions_2

Software:

TOPSPIN, Bruker Biospin - collection, processing

SPARKY, Goddard - chemical shift assignment

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

AMBER v9, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement, structure solution

NMR spectrometers:

Bruker Avance 500 MHz
Bruker Avance 600 MHz
Bruker Avance 900 MHz