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Found 1 Document (1.048 seconds)

BMRB: 25799

2N7B

NMR structure of human I-type lectin domain-glycan complex

Authors

Proepster, J.M., Yang, F., Rabbani, S., Ernst, B., Allain, F.H.-T., Schubert, M.

Assembly

human I-type lectin domain-glycan complex

Entity

1. Siglec-8 (polymer, Thiol state: all disulfide bound), 145 monomers, 16645.29 Da Detail

MEGDRQYGDG YLLQVQELVT VQEGLSVHVP CSFSYPQDGW TDSDPVHGYW FRAGDRPYQD APVATNNPDR EVQAETQGRF QLLGDIWSND CSLSIRDARK RDKGSYFFRL ERGSMKWSYK SQLNYKTKQL SVFVTALTHG SLVPR

2. SUGAR (5-MER) (non-polymer), 5 monomers, 957.9019 Da

Total weight

17603.191 Da

Max. entity weight

16645.29 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS31:SG	1:CYS91:SG

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 96.7 %, Completeness: 95.4 %, Completeness (bb): 97.0 % Detail

Polymer type: polypeptide(L) polysaccharide(D)

	Total	¹H	¹³C	¹⁵N
All	95.4 % (1625 of 1703)	96.3 % (856 of 889)	94.2 % (619 of 657)	95.5 % (150 of 157)
Backbone	97.0 % (830 of 856)	95.9 % (283 of 295)	98.3 % (416 of 423)	94.9 % (131 of 138)
Sidechain	94.5 % (926 of 980)	96.5 % (573 of 594)	91.0 % (334 of 367)	100.0 % (19 of 19)
Aromatic	82.6 % (152 of 184)	95.7 % (88 of 92)	68.2 % (60 of 88)	100.0 % (4 of 4)
Methyl	97.6 % (123 of 126)	96.8 % (61 of 63)	98.4 % (62 of 63)

1. Siglec-8

MEGDRQYGDG YLLQVQELVT VQEGLSVHVP CSFSYPQDGW TDSDPVHGYW FRAGDRPYQD APVATNNPDR EVQAETQGRF QLLGDIWSND CSLSIRDARK RDKGSYFFRL ERGSMKWSYK SQLNYKTKQL SVFVTALTHG SLVPR

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
7	Siglec-8	[U-100% 13C; U-100% 15N]	protein	0.3 ~ 1.2 mM
8	potassium phosphate	natural abundance	buffer	20 mM
9	sodium chloride	natural abundance	salt	40 mM
10	SUGAR (5-MER)	natural abundance		0.7 ~ 2.4 mM
11	D2O	[U-2H]	solvent	5 %
12	H2O	natural abundance	solvent	95 %

Chem. Shift Complete2

Sequence coverage: 28.7 %, Completeness: 56.8 %, Completeness (bb): 59.7 % Detail

Polymer type: polypeptide(L) polysaccharide(D)

	Total	¹H	¹³C	¹⁵N
All	56.8 % (1934 of 3406)	56.5 % (1004 of 1778)	56.4 % (741 of 1314)	60.2 % (189 of 314)
Backbone	59.7 % (1022 of 1712)	59.0 % (348 of 590)	59.6 % (504 of 846)	61.6 % (170 of 276)
Sidechain	54.7 % (1072 of 1960)	55.2 % (656 of 1188)	54.1 % (397 of 734)	50.0 % (19 of 38)
Aromatic	43.5 % (160 of 368)	50.0 % (92 of 184)	36.4 % (64 of 176)	50.0 % (4 of 8)
Methyl	59.5 % (150 of 252)	60.3 % (76 of 126)	58.7 % (74 of 126)

1. Siglec-8

MEGDRQYGDG YLLQVQELVT VQEGLSVHVP CSFSYPQDGW TDSDPVHGYW FRAGDRPYQD APVATNNPDR EVQAETQGRF QLLGDIWSND CSLSIRDARK RDKGSYFFRL ERGSMKWSYK SQLNYKTKQL SVFVTALTHG SLVPR

Show sample condition

Sample

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
13	Siglec-8	[U-100% 13C; U-100% 15N]	protein	0.3 ~ 1.2 mM
14	potassium phosphate	natural abundance	buffer	20 mM
15	sodium chloride	natural abundance	salt	40 mM
16	SUGAR (5-MER)	natural abundance		0.7 ~ 2.4 mM
17	D2O	[U-2H]	solvent	100 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2N7B, Strand ID: A Detail

Release date

2016-07-04

Citation

Structural basis for sulfation-dependent self-glycan recognition by the human immune-inhibitory receptor Siglec-8
Proepster, J.M., Yang, F., Rabbani, S., Ernst, B., Allain, F.H.-T., Schubert, M.
Proc. Natl. Acad. Sci. U. S. A. (2016), 113, 4170-4179, PubMed 27357658 , DOI 10.1073/pnas.1602214113 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 25798 released on 2016-07-04
Title NMR structure of human I-type lectin domain

Related entities 1. Siglec-8, : 1 : 3 : 3 : 64 entities Detail

Interaction partners 1. Siglec-8, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 20 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	Siglec-8	[U-100% 15N]	protein	0.7 ~ 1.2 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	40 mM
4	SUGAR (5-MER)	natural abundance		0.7 ~ 2.4 mM
5	D2O	[U-2H]	solvent	5 %
6	H2O	natural abundance	solvent	95 %

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, pH 7.4

#	Name	Isotope labeling	Type	Concentration
7	Siglec-8	[U-100% 13C; U-100% 15N]	protein	0.3 ~ 1.2 mM
8	potassium phosphate	natural abundance	buffer	20 mM
9	sodium chloride	natural abundance	salt	40 mM
10	SUGAR (5-MER)	natural abundance		0.7 ~ 2.4 mM
11	D2O	[U-2H]	solvent	5 %
12	H2O	natural abundance	solvent	95 %

3 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, pH 7.4

#	Name	Isotope labeling	Type	Concentration
7	Siglec-8	[U-100% 13C; U-100% 15N]	protein	0.3 ~ 1.2 mM
8	potassium phosphate	natural abundance	buffer	20 mM
9	sodium chloride	natural abundance	salt	40 mM
10	SUGAR (5-MER)	natural abundance		0.7 ~ 2.4 mM
11	D2O	[U-2H]	solvent	5 %
12	H2O	natural abundance	solvent	95 %

4 3D HNCA

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
7	Siglec-8	[U-100% 13C; U-100% 15N]	protein	0.3 ~ 1.2 mM
8	potassium phosphate	natural abundance	buffer	20 mM
9	sodium chloride	natural abundance	salt	40 mM
10	SUGAR (5-MER)	natural abundance		0.7 ~ 2.4 mM
11	D2O	[U-2H]	solvent	5 %
12	H2O	natural abundance	solvent	95 %

5 3D HNCACB

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
7	Siglec-8	[U-100% 13C; U-100% 15N]	protein	0.3 ~ 1.2 mM
8	potassium phosphate	natural abundance	buffer	20 mM
9	sodium chloride	natural abundance	salt	40 mM
10	SUGAR (5-MER)	natural abundance		0.7 ~ 2.4 mM
11	D2O	[U-2H]	solvent	5 %
12	H2O	natural abundance	solvent	95 %

6 3D CBCA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
7	Siglec-8	[U-100% 13C; U-100% 15N]	protein	0.3 ~ 1.2 mM
8	potassium phosphate	natural abundance	buffer	20 mM
9	sodium chloride	natural abundance	salt	40 mM
10	SUGAR (5-MER)	natural abundance		0.7 ~ 2.4 mM
11	D2O	[U-2H]	solvent	5 %
12	H2O	natural abundance	solvent	95 %

7 3D HNCO

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
7	Siglec-8	[U-100% 13C; U-100% 15N]	protein	0.3 ~ 1.2 mM
8	potassium phosphate	natural abundance	buffer	20 mM
9	sodium chloride	natural abundance	salt	40 mM
10	SUGAR (5-MER)	natural abundance		0.7 ~ 2.4 mM
11	D2O	[U-2H]	solvent	5 %
12	H2O	natural abundance	solvent	95 %

8 3D HN(CO)CA

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
7	Siglec-8	[U-100% 13C; U-100% 15N]	protein	0.3 ~ 1.2 mM
8	potassium phosphate	natural abundance	buffer	20 mM
9	sodium chloride	natural abundance	salt	40 mM
10	SUGAR (5-MER)	natural abundance		0.7 ~ 2.4 mM
11	D2O	[U-2H]	solvent	5 %
12	H2O	natural abundance	solvent	95 %

9 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
13	Siglec-8	[U-100% 13C; U-100% 15N]	protein	0.3 ~ 1.2 mM
14	potassium phosphate	natural abundance	buffer	20 mM
15	sodium chloride	natural abundance	salt	40 mM
16	SUGAR (5-MER)	natural abundance		0.7 ~ 2.4 mM
17	D2O	[U-2H]	solvent	100 %

10 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
7	Siglec-8	[U-100% 13C; U-100% 15N]	protein	0.3 ~ 1.2 mM
8	potassium phosphate	natural abundance	buffer	20 mM
9	sodium chloride	natural abundance	salt	40 mM
10	SUGAR (5-MER)	natural abundance		0.7 ~ 2.4 mM
11	D2O	[U-2H]	solvent	5 %
12	H2O	natural abundance	solvent	95 %

11 2D 1H-1H NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, pH 7.4

#	Name	Isotope labeling	Type	Concentration
18	Siglec-8	[U-100% 15N]	protein	0.3 ~ 1.2 mM
19	potassium phosphate	natural abundance	buffer	20 mM
20	sodium chloride	natural abundance	salt	40 mM
21	SUGAR (5-MER)	natural abundance		0.7 ~ 2.4 mM
22	D2O	[U-2H]	solvent	100 %

12 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
7	Siglec-8	[U-100% 13C; U-100% 15N]	protein	0.3 ~ 1.2 mM
8	potassium phosphate	natural abundance	buffer	20 mM
9	sodium chloride	natural abundance	salt	40 mM
10	SUGAR (5-MER)	natural abundance		0.7 ~ 2.4 mM
11	D2O	[U-2H]	solvent	5 %
12	H2O	natural abundance	solvent	95 %

13 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
7	Siglec-8	[U-100% 13C; U-100% 15N]	protein	0.3 ~ 1.2 mM
8	potassium phosphate	natural abundance	buffer	20 mM
9	sodium chloride	natural abundance	salt	40 mM
10	SUGAR (5-MER)	natural abundance		0.7 ~ 2.4 mM
11	D2O	[U-2H]	solvent	5 %
12	H2O	natural abundance	solvent	95 %

14 2D 1H-1H TOCSY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
18	Siglec-8	[U-100% 15N]	protein	0.3 ~ 1.2 mM
19	potassium phosphate	natural abundance	buffer	20 mM
20	sodium chloride	natural abundance	salt	40 mM
21	SUGAR (5-MER)	natural abundance		0.7 ~ 2.4 mM
22	D2O	[U-2H]	solvent	100 %

15 2D 13C F2-filtered NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, pH 7.4

#	Name	Isotope labeling	Type	Concentration
13	Siglec-8	[U-100% 13C; U-100% 15N]	protein	0.3 ~ 1.2 mM
14	potassium phosphate	natural abundance	buffer	20 mM
15	sodium chloride	natural abundance	salt	40 mM
16	SUGAR (5-MER)	natural abundance		0.7 ~ 2.4 mM
17	D2O	[U-2H]	solvent	100 %

16 2D 13C F1-filtered TOCSY

Instrument

Bruker Avance - 750 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
13	Siglec-8	[U-100% 13C; U-100% 15N]	protein	0.3 ~ 1.2 mM
14	potassium phosphate	natural abundance	buffer	20 mM
15	sodium chloride	natural abundance	salt	40 mM
16	SUGAR (5-MER)	natural abundance		0.7 ~ 2.4 mM
17	D2O	[U-2H]	solvent	100 %

17 2D 13C F1-filtered TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
7	Siglec-8	[U-100% 13C; U-100% 15N]	protein	0.3 ~ 1.2 mM
8	potassium phosphate	natural abundance	buffer	20 mM
9	sodium chloride	natural abundance	salt	40 mM
10	SUGAR (5-MER)	natural abundance		0.7 ~ 2.4 mM
11	D2O	[U-2H]	solvent	5 %
12	H2O	natural abundance	solvent	95 %

18 2D 13C F1-filtered F2-filtered NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
13	Siglec-8	[U-100% 13C; U-100% 15N]	protein	0.3 ~ 1.2 mM
14	potassium phosphate	natural abundance	buffer	20 mM
15	sodium chloride	natural abundance	salt	40 mM
16	SUGAR (5-MER)	natural abundance		0.7 ~ 2.4 mM
17	D2O	[U-2H]	solvent	100 %

19 3D 13C F1-edited F3-filtered NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
13	Siglec-8	[U-100% 13C; U-100% 15N]	protein	0.3 ~ 1.2 mM
14	potassium phosphate	natural abundance	buffer	20 mM
15	sodium chloride	natural abundance	salt	40 mM
16	SUGAR (5-MER)	natural abundance		0.7 ~ 2.4 mM
17	D2O	[U-2H]	solvent	100 %

20 2D 13C/15N F2-filtered NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	Siglec-8	[U-100% 15N]	protein	0.7 ~ 1.2 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	40 mM
4	SUGAR (5-MER)	natural abundance		0.7 ~ 2.4 mM
5	D2O	[U-2H]	solvent	5 %
6	H2O	natural abundance	solvent	95 %

nullKeywords I-type lectin, SAF-2, Sialic acid-binding immunoglobulin-like lectin 8, Siglec8, carbohydrate recognition, carbohydrate-binding receptor, protein/glycan complex, sulfated sialyl Lewis X

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Found 1 Document (1.048 seconds)

BMRB: 25799

Sample

Sample

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. Siglec-8, : 1 : 3 : 3 : 64 entities Detail

Interaction partners 1. Siglec-8, : 1 interactors Detail

Experiments performed 20 experiments Detail

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