BMRBj - BMREntryMaster

Found 1 Document (1.111 seconds)

BMRB: 25798

2N7A

NMR structure of human I-type lectin domain

Authors

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

Assembly

human Siglec-8

Entity

1. human 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

Formula 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 Complete

Sequence coverage: 100.0 %, Completeness: 94.7 %, Completeness (bb): 96.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.7 % (1612 of 1703)	95.3 % (847 of 889)	93.3 % (613 of 657)	96.8 % (152 of 157)
Backbone	96.7 % (828 of 856)	96.3 % (284 of 295)	97.2 % (411 of 423)	96.4 % (133 of 138)
Sidechain	93.2 % (913 of 980)	94.8 % (563 of 594)	90.2 % (331 of 367)	100.0 % (19 of 19)
Aromatic	81.5 % (150 of 184)	95.7 % (88 of 92)	65.9 % (58 of 88)	100.0 % (4 of 4)
Methyl	98.4 % (124 of 126)	96.8 % (61 of 63)	100.0 % (63 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 7.0

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

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.0 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.0 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.09 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.73 ppm, Outliers: 6 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2N7A, 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: 25799 released on 2016-07-04
Title NMR structure of human I-type lectin domain-glycan complex

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

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

More details for 1 interactors identified by 1 citations

Experiments performed 15 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Siglec-8	[U-100% 15N]	protein	0.3 ~ 1.2 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	40 mM
4	D2O	[U-2H]	solvent	5 %
5	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, Temperature 293 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
6	Siglec-8	[U-100% 13C; U-100% 15N]	protein	0.3 ~ 1.2 mM
7	potassium phosphate	natural abundance	buffer	20 mM
8	sodium chloride	natural abundance	salt	40 mM
9	D2O	[U-2H]	solvent	5 %
10	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, Temperature 293 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
6	Siglec-8	[U-100% 13C; U-100% 15N]	protein	0.3 ~ 1.2 mM
7	potassium phosphate	natural abundance	buffer	20 mM
8	sodium chloride	natural abundance	salt	40 mM
9	D2O	[U-2H]	solvent	5 %
10	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 7.0

#	Name	Isotope labeling	Type	Concentration
6	Siglec-8	[U-100% 13C; U-100% 15N]	protein	0.3 ~ 1.2 mM
7	potassium phosphate	natural abundance	buffer	20 mM
8	sodium chloride	natural abundance	salt	40 mM
9	D2O	[U-2H]	solvent	5 %
10	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 7.0

#	Name	Isotope labeling	Type	Concentration
6	Siglec-8	[U-100% 13C; U-100% 15N]	protein	0.3 ~ 1.2 mM
7	potassium phosphate	natural abundance	buffer	20 mM
8	sodium chloride	natural abundance	salt	40 mM
9	D2O	[U-2H]	solvent	5 %
10	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 7.0

#	Name	Isotope labeling	Type	Concentration
6	Siglec-8	[U-100% 13C; U-100% 15N]	protein	0.3 ~ 1.2 mM
7	potassium phosphate	natural abundance	buffer	20 mM
8	sodium chloride	natural abundance	salt	40 mM
9	D2O	[U-2H]	solvent	5 %
10	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 7.0

#	Name	Isotope labeling	Type	Concentration
6	Siglec-8	[U-100% 13C; U-100% 15N]	protein	0.3 ~ 1.2 mM
7	potassium phosphate	natural abundance	buffer	20 mM
8	sodium chloride	natural abundance	salt	40 mM
9	D2O	[U-2H]	solvent	5 %
10	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 7.0

#	Name	Isotope labeling	Type	Concentration
6	Siglec-8	[U-100% 13C; U-100% 15N]	protein	0.3 ~ 1.2 mM
7	potassium phosphate	natural abundance	buffer	20 mM
8	sodium chloride	natural abundance	salt	40 mM
9	D2O	[U-2H]	solvent	5 %
10	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 7.0

#	Name	Isotope labeling	Type	Concentration
16	Siglec-8	[U-100% 13C; U-100% 15N]	protein	0.3 ~ 1.2 mM
17	potassium phosphate	natural abundance	buffer	20 mM
18	sodium chloride	natural abundance	salt	40 mM
19	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 7.0

#	Name	Isotope labeling	Type	Concentration
6	Siglec-8	[U-100% 13C; U-100% 15N]	protein	0.3 ~ 1.2 mM
7	potassium phosphate	natural abundance	buffer	20 mM
8	sodium chloride	natural abundance	salt	40 mM
9	D2O	[U-2H]	solvent	5 %
10	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, Temperature 293 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
20	Siglec-8	[U-100% 15N]	protein	0.3 ~ 1.2 mM
21	potassium phosphate	natural abundance	buffer	20 mM
22	sodium chloride	natural abundance	salt	40 mM
23	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 7.0

#	Name	Isotope labeling	Type	Concentration
6	Siglec-8	[U-100% 13C; U-100% 15N]	protein	0.3 ~ 1.2 mM
7	potassium phosphate	natural abundance	buffer	20 mM
8	sodium chloride	natural abundance	salt	40 mM
9	D2O	[U-2H]	solvent	5 %
10	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 7.0

#	Name	Isotope labeling	Type	Concentration
6	Siglec-8	[U-100% 13C; U-100% 15N]	protein	0.3 ~ 1.2 mM
7	potassium phosphate	natural abundance	buffer	20 mM
8	sodium chloride	natural abundance	salt	40 mM
9	D2O	[U-2H]	solvent	5 %
10	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 7.0

#	Name	Isotope labeling	Type	Concentration
20	Siglec-8	[U-100% 15N]	protein	0.3 ~ 1.2 mM
21	potassium phosphate	natural abundance	buffer	20 mM
22	sodium chloride	natural abundance	salt	40 mM
23	D2O	[U-2H]	solvent	100 %

15 2D 1H-13C constant-time HSQC to obtain stereospecific assignments of Val/Leu methyls

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
11	Siglec-8	[U-10% 13C; U-100% 15N]	protein	0.3 mM
12	potassium phosphate	natural abundance	buffer	20 mM
13	sodium chloride	natural abundance	salt	40 mM
14	D2O	[U-2H]	solvent	5 %
15	H2O	natural abundance	solvent	95 %

nullKeywords I-type lectin, SAF-2, Sialic acid-binding immunoglobulin-like lectin 8, Siglec8, carbohydrate-binding receptor

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Found 1 Document (1.111 seconds)

BMRB: 25798

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1 entries Detail

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

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

Experiments performed 15 experiments Detail

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