BMRB Entry 25046

Name: Backbone 1H, 15N Chemical Shift Assignments of the DC-SIGNR carbohydrate recognition domain in the Apo state.
Published: 2014-07-25

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25046

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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:

Backbone 1H, 15N Chemical Shift Assignments of the DC-SIGNR carbohydrate recognition domain in the Apo state.

Deposition date:

2014-06-25

Original release date:

2014-07-25

Authors:

Probert, Fay; Dixon, Ann; Mitchell, Dan

Citation:

Citation: Probert, Fay; Dixon, Ann; Mitchell, Dan. "NMR evidence for oligosaccharide release from the DC-SIGNR (CLEC4M) carbohydrate recognition domain at low pH" FEBS J. ., .-..

Assembly members:

Assembly members:
DC-SIGNR, polymer, 139 residues, 16194.7 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: AERLCRHCPKDWTFFQGNCY FMSNSQRNWHDSVTACQEVR AQLVVIKTAEEQNFLQLQTS RSNRFSWMGLSDLNQEGTWQ WVDGSPLSPSFQRYWNSGEP NNSGNEDCAEFSGSGWNDNR CDVDNYWICKKPAACFRDE

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	84
15N chemical shifts	84

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DC-SIGNR CRD	1

Entities:

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

1

ALA

GLU

ARG

LEU

CYS

ARG

HIS

CYS

PRO

LYS

2

ASP

TRP

THR

PHE

GLN

GLY

ASN

CYS

TYR

3

PHE

MET

SER

ASN

SER

GLN

ARG

ASN

TRP

HIS

4

ASP

SER

VAL

THR

ALA

CYS

GLN

GLU

VAL

ARG

5

ALA

GLN

LEU

VAL

ILE

LYS

THR

ALA

GLU

6

GLU

GLN

ASN

PHE

LEU

GLN

LEU

GLN

THR

SER

7

ARG

SER

ASN

ARG

PHE

SER

TRP

MET

GLY

LEU

8

SER

ASP

LEU

ASN

GLN

GLU

GLY

THR

TRP

GLN

9

TRP

VAL

ASP

GLY

SER

PRO

LEU

SER

PRO

SER

10

PHE

GLN

ARG

TYR

TRP

ASN

SER

GLY

GLU

PRO

11

ASN

SER

GLY

ASN

GLU

ASP

CYS

ALA

GLU

12

PHE

SER

GLY

SER

GLY

TRP

ASN

ASP

ASN

ARG

13

CYS

ASP

VAL

ASP

ASN

TYR

TRP

ILE

CYS

LYS

14

LYS

PRO

ALA

CYS

PHE

ARG

ASP

GLU

Samples:

sample_1: DC-SIGNR, [U-100% 15N], 0.7 mM; HEPES, [U-100% 2H], 20 mM; NaCl 20 mM; H2O 90%; D2O 10%

sample_conditions_1: temperature: 310 K; pH: 6.8; pressure: 1 atm

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection, processing

SPARKY, Goddard - chemical shift assignment, peak picking

NMR spectrometers:

Bruker Avance 700 MHz

NCBI	9606
BMRB	19297
PDB	1K9J 1SL6 1XAR 1XPH
DBJ	BAF84967 BAG65307
GB	AAG13815 AAG13848 AAH38851 AAI10615 AAK20998
REF	NP_001138376 NP_001138377 NP_001138378 NP_001138379 NP_001138381
SP	Q8HY06 Q9H2X3
AlphaFold	Q8HY06 Q9H2X3