BMRB Entry 18704

Name: human Siglec5 Carbohydrate Recognition Domain Chemical Shifts
Published: 2012-09-07

Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR18704

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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:

human Siglec5 Carbohydrate Recognition Domain Chemical Shifts

Deposition date:

2012-09-06

Original release date:

2012-09-07

Authors:

Barb, Adam; Prestegard, James

Citation:

Citation: Barb, Adam; Wang, Xu; Prestegard, James. "NMR chemical shift mapping of refolded human sialic-acid-binding immunoglobulin-like lectin 5 binding to complex carbohydrates" .

Assembly members:

Assembly members:
Siglec5, polymer, 143 residues, Formula weight is not available

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: pet28b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Siglec5: MGSSHHHHHHSSGLVPRGSH PVYELQVQKSVTVQEGLAVL VPCSFSYPWRSWYSSPPLYV YWFRDGEIPYYAEVVATNNP DRRVKPETQGRFRLLGDVQK KNCSLSIGDARMEDTGSYFF RVERGRDVKYSYQQNKLNLE VTA

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	330
15N chemical shifts	110
1H chemical shifts	110

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Siglec5	1

Entities:

Entity 1, Siglec5 143 residues - Formula weight is not available

This construct encodes residues P19 to A141 of human siglec5; from Uniprot DB: O15389

1

MET

GLY

SER

HIS

2

SER

GLY

LEU

VAL

PRO

ARG

GLY

SER

HIS

3

PRO

VAL

TYR

GLU

LEU

GLN

VAL

GLN

LYS

SER

4

VAL

THR

VAL

GLN

GLU

GLY

LEU

ALA

VAL

LEU

5

VAL

PRO

CYS

SER

PHE

SER

TYR

PRO

TRP

ARG

6

SER

TRP

TYR

SER

PRO

LEU

TYR

VAL

7

TYR

TRP

PHE

ARG

ASP

GLY

GLU

ILE

PRO

TYR

8

TYR

ALA

GLU

VAL

ALA

THR

ASN

PRO

9

ASP

ARG

VAL

LYS

PRO

GLU

THR

GLN

GLY

10

ARG

PHE

ARG

LEU

GLY

ASP

VAL

GLN

LYS

11

LYS

ASN

CYS

SER

LEU

SER

ILE

GLY

ASP

ALA

12

ARG

MET

GLU

ASP

THR

GLY

SER

TYR

PHE

13

ARG

VAL

GLU

ARG

GLY

ARG

ASP

VAL

LYS

TYR

14

SER

TYR

GLN

ASN

LYS

LEU

ASN

LEU

GLU

15

VAL

THR

ALA

Samples:

sample_1: Siglec5, [U-99% 13C; U-99% 15N], 0.2 – 0.4 mM; Arg 50 mM; Glu 50 mM; NaCl 150 mM; imidazole 10 mM

sample_2: Siglec5, [U-100% 13C; U-100% 15N; U-80% 2H], 0.2 mM; Arg 50 mM; Glu 50 mM; NaCl 150 mM; imidazole 10 mM

sample_conditions_1: ionic strength: 260 mM; pH: 6.5; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	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_2	isotropic	sample_conditions_1
3D HN(COCA)CB	sample_2	isotropic	sample_conditions_1

Software:

NMRView, Johnson, One Moon Scientific - chemical shift assignment

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

NMR spectrometers:

Varian INOVA 600 MHz
Varian INOVA 800 MHz
Varian VXRS 900 MHz

PDB	2ZG1 2ZG2 2ZG3
DBJ	BAG60544
GB	AAB70703 AAD50978 AAF87846 AAH29896 AAK77223
REF	NP_001092082 NP_003821 XP_006723021 XP_011524598 XP_011524599
SP	O15389 Q08ET2
AlphaFold	O15389 Q08ET2