BMRB Entry 27854

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR27854

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Title:
Human DC-SIGN Carbohydrate Recognition Domain
Deposition date:
2019-03-26
Original release date:
2019-07-18
Authors:
Valverde, Pablo; Delgado, Sandra; Martinez, J.Daniel; Jimenez-Barbero, Jesus; Arda, Ana
Citation:

Citation: Valverde, Pablo; Delgado, Sandra; Martinez, J.Daniel; Vendeville, Jean-Baptiste; Malassis, Julien; Linclau, Bruno; Reichardt, Niels-Christian; Canada, F.Javier; Jimenez-Barbero, Jesus; Arda, Ana. "Molecular Insights into DC-SIGN Binding to Self-Antigens: The Interaction with the Blood Group A/B Antigens"  ACS Chem Biol. 14, 1660-1671 (2019).
PubMed: 31283166

Assembly members:

Assembly members:
DC-SIGN_CRD, polymer, 177 residues, 20097 Da.
entity_CA, 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: pET15b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DC-SIGN_CRD: MGSSHHHHHHSSGLVPRGSH MAERLCHPCPWEWTFFQGNC YFMSNSQRNWHDSITACKEV GAQLVVIKSAEEQNFLQLQS SRSNRFTWMGLSDLNQEGTW QWVDGSPLLPSFKQYWNRGE PNNVGEEDCAEFSGNGWNDD KCNLAKFWICKKSAASCSRD EEQFLSPAPATPNPPPA

Data sets:
Data typeCount
13C chemical shifts334
15N chemical shifts232
1H chemical shifts232

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1DC-SIGN CRD1
2Calcium ion2

Entities:

Entity 1, DC-SIGN CRD 177 residues - 20097 Da.

Residues 1-26 (228-253) represent a non-native affinity tag. Residues 27-177 correspond to residues 254-404 in PDB 1SL5 (CRD domain).

1   METGLYSERSERHISHISHISHISHISHIS
2   SERSERGLYLEUVALPROARGGLYSERHIS
3   METALAGLUARGLEUCYSHISPROCYSPRO
4   TRPGLUTRPTHRPHEPHEGLNGLYASNCYS
5   TYRPHEMETSERASNSERGLNARGASNTRP
6   HISASPSERILETHRALACYSLYSGLUVAL
7   GLYALAGLNLEUVALVALILELYSSERALA
8   GLUGLUGLNASNPHELEUGLNLEUGLNSER
9   SERARGSERASNARGPHETHRTRPMETGLY
10   LEUSERASPLEUASNGLNGLUGLYTHRTRP
11   GLNTRPVALASPGLYSERPROLEULEUPRO
12   SERPHELYSGLNTYRTRPASNARGGLYGLU
13   PROASNASNVALGLYGLUGLUASPCYSALA
14   GLUPHESERGLYASNGLYTRPASNASPASP
15   LYSCYSASNLEUALALYSPHETRPILECYS
16   LYSLYSSERALAALASERCYSSERARGASP
17   GLUGLUGLNPHELEUSERPROALAPROALA
18   THRPROASNPROPROPROALA

Entity 2, Calcium ion - Ca - 40.078 Da.

1   CA

Samples:

CRD_D-Mannose: DC-SIGN CRD, [U-13C; U-15N], 225 uM; TRIS 25 mM; sodium chloride 150 mM; calcium chloride 4 mM; DTT 2 mM; D-Mannose 30 mM

Free_CRD: DC-SIGN CRD, [U-13C; U-15N], 200 uM; TRIS 25 mM; sodium chloride 150 mM; calcium chloride 4 mM; DTT 2 mM

sample_conditions_1: ionic strength: 0.351 M; pH: 8; pressure: 1 atm; temperature: 310 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCFree_CRDisotropicsample_conditions_1
3D HNCAFree_CRDisotropicsample_conditions_1
3D HN(CO)CAFree_CRDisotropicsample_conditions_1
3D CBCA(CO)NHFree_CRDisotropicsample_conditions_1
2D 1H-15N HSQCCRD_D-Mannoseisotropicsample_conditions_1
3D CBCA(CO)NHCRD_D-Mannoseisotropicsample_conditions_1
3D HNCACBCRD_D-Mannoseisotropicsample_conditions_1

Software:

TOPSPIN v3.5, Bruker Biospin - collection, processing

CARANMR v1.9.1.0, Keller and Wuthrich - chemical shift assignment, data analysis, peak picking

NMR spectrometers:

  • Bruker Avance 800 MHz

Related Database Links:

PDB

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