BMRB Entry 19297

Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR19297

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Title:
Chemical shift assignments of the human C-type lectin DC-SIGNR (Dendritic Cell-Specific Intercellular adhesion molecule-3-Grabbing Non-integrin related) carbohydrate recognition domain in the holo (calcium bound) form.
Deposition date:
2013-06-11
Original release date:
2013-06-28
Authors:
Probert, Fay; Whittaker, Sara; Mitchell, Daniel; Dixon, Ann
Citation:

Citation: Probert, Fay; Whittaker, Sara B-M; Crispin, Max; Mitchell, Daniel; Dixon, Ann. "Solution NMR analyses of the C-type carbohydrate recognition domain of DC-SIGNR protein reveal different binding modes for HIV-derived oligosaccharides and smaller glycan fragments."  J. Biol. Chem. 288, 22745-22757 (2013).
PubMed: 23788638

Assembly members:

Assembly members:
DC-SIGNR_carbohydrate_recognition_domain, polymer, 139 residues, 16194.7 Da.
CALCIUM ION, non-polymer, 40.078 Da.

Natural source:

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pT5T

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DC-SIGNR_carbohydrate_recognition_domain: AERLCRHCPKDWTFFQGNCY FMSNSQRNWHDSVTACQEVR AQLVVIKTAEEQNFLQLQTS RSNRFSWMGLSDLNQEGTWQ WVDGSPLSPSFQRYWNSGEP NNSGNEDCAEFSGSGWNDNR CDVDNYWICKKPAACFRDE

Data sets:
Data typeCount
13C chemical shifts431
15N chemical shifts116
1H chemical shifts501

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1DC-SIGNR CRD1
2Ca ion, 12
3Ca ion, 22
4Ca ion, 32

Entities:

Entity 1, DC-SIGNR CRD 139 residues - 16194.7 Da.

N-terminal Ala residue incorporated from bacterial expression protocol.

1   ALAGLUARGLEUCYSARGHISCYSPROLYS
2   ASPTRPTHRPHEPHEGLNGLYASNCYSTYR
3   PHEMETSERASNSERGLNARGASNTRPHIS
4   ASPSERVALTHRALACYSGLNGLUVALARG
5   ALAGLNLEUVALVALILELYSTHRALAGLU
6   GLUGLNASNPHELEUGLNLEUGLNTHRSER
7   ARGSERASNARGPHESERTRPMETGLYLEU
8   SERASPLEUASNGLNGLUGLYTHRTRPGLN
9   TRPVALASPGLYSERPROLEUSERPROSER
10   PHEGLNARGTYRTRPASNSERGLYGLUPRO
11   ASNASNSERGLYASNGLUASPCYSALAGLU
12   PHESERGLYSERGLYTRPASNASPASNARG
13   CYSASPVALASPASNTYRTRPILECYSLYS
14   LYSPROALAALACYSPHEARGASPGLU

Entity 2, Ca ion, 1 - Ca - 40.078 Da.

1   CA

Samples:

sample_1: DC-SIGNR carbohydrate recognition domain, [U-100% 13C; U-100% 15N], 0.7 mM; HEPES, [U-100% 2H], 20 mM; calcium chloride 4 mM; sodium chloride 20 mM; H2O 90%; D2O 10%

sample_conditions_1: pH: 6.8; pressure: 1 atm; temperature: 310.15 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1

Software:

TOPSPIN v2.0, Bruker Biospin - collection, processing

SPARKY v3, Goddard - chemical shift assignment, peak picking

NMR spectrometers:

  • Bruker Avance 700 MHz
  • Varian Unity 800 MHz

Related Database Links:

UNP Q9H2X3
BMRB 25046
PDB
DBJ BAF84967 BAG65307
GB AAG13815 AAG13848 AAH38851 AAI10615 AAK20998
REF NP_001138376 NP_001138377 NP_001138378 NP_001138379 NP_001138381
SP Q8HY06 Q9H2X3
AlphaFold Q9Y2A8 Q8HY06 Q9H2X3

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks