BMRB Entry 19931

Name: DC-SIGN
Published: 2014-05-27

Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR19931

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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:

DC-SIGN

Deposition date:

2014-04-23

Original release date:

2014-05-27

Authors:

Pederson, Kari; Prestegard, James

Citation:

Citation: Pederson, Kari; Mitchell, Daniel; Prestegard, James. "Structural Characterization of the DC-SIGN-LewisX Complex" Biochemistry ., .-..

Assembly members:

Assembly members:
DC-SIGN, polymer, 177 residues, 20097.2 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: peT28a

Entity Sequences (FASTA):

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

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	364
15N chemical shifts	122
1H chemical shifts	122

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DC-SIGN	1
2	CA_1	2
3	CA_2	2
4	CA_3	2

Entities:

Entity 1, DC-SIGN 177 residues - 20097.2 Da.

1

MET

GLY

SER

HIS

2

SER

GLY

LEU

VAL

PRO

ARG

GLY

SER

HIS

3

MET

ALA

GLU

ARG

LEU

CYS

HIS

PRO

CYS

PRO

4

TRP

GLU

TRP

THR

PHE

GLN

GLY

ASN

CYS

5

TYR

PHE

MET

SER

ASN

SER

GLN

ARG

ASN

TRP

6

HIS

ASP

SER

ILE

THR

ALA

CYS

LYS

GLU

VAL

7

GLY

ALA

GLN

LEU

VAL

ILE

LYS

SER

ALA

8

GLU

GLN

ASN

PHE

LEU

GLN

LEU

GLN

SER

9

SER

ARG

SER

ASN

ARG

PHE

THR

TRP

MET

GLY

10

LEU

SER

ASP

LEU

ASN

GLN

GLU

GLY

THR

TRP

11

GLN

TRP

VAL

ASP

GLY

SER

PRO

LEU

PRO

12

SER

PHE

LYS

GLN

TYR

TRP

ASN

ARG

GLY

GLU

13

PRO

ASN

VAL

GLY

GLU

ASP

CYS

ALA

14

GLU

PHE

SER

GLY

ASN

GLY

TRP

ASN

ASP

15

LYS

CYS

ASN

LEU

ALA

LYS

PHE

TRP

ILE

CYS

16

LYS

SER

ALA

SER

CYS

SER

ARG

ASP

17

GLU

GLN

PHE

LEU

SER

PRO

ALA

PRO

ALA

18

THR

PRO

ASN

PRO

ALA

Entity 2, CA_1 - Ca - 40.078 Da.

1

CA

Samples:

NC_sample: DC-SIGN, [U-100% 13C; U-100% 15N], 100 – 400 uM; D2O 10%; H2O 90%

high_temperature: ionic strength: 100 mM; pH: 7.5; pressure: 1 atm; temperature: 310 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	NC_sample	isotropic	high_temperature
3D CBCA(CO)NH	NC_sample	isotropic	high_temperature
3D HNCA	NC_sample	isotropic	high_temperature
3D HNCACB	NC_sample	isotropic	high_temperature
3D HNCO	NC_sample	isotropic	high_temperature

Software:

SPARKY v3.113, Goddard - chemical shift assignment, peak picking

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMR spectrometers:

Varian INOVA 600 MHz

EMBL	CD209_HUMAN
PDB	1K9I 1SL4 1SL5 2B6B 2IT5 2IT6 2XR5 2XR6
DBJ	BAF85778 BAG36354 BAG65070 BAI45727
GB	AAF77072 AAG13814 AAI10616 AAK20997 AAK91846
REF	NP_001138365 NP_001138366 NP_001138367 NP_001138368 NP_001138371
SP	Q8HY00 Q9NNX6
AlphaFold	Q8HY00 Q9NNX6