BMRBj - BMREntryMaster

Found 1 Document (4.524 seconds)

BMRB: 5194

1K5W

Three-dimensional Structure of the Synaptotagmin 1 C2B-domain: Synaptotagmin 1 as a Phospholipid Binding Machine

Authors

Fernandez, I., Arac, D., Ubach, J., Gerber, S.H., Shin, O., Gao, Y., Anderson, R.G.W., Sudhof, T.C., Rizo, J.

Assembly

Synaptotagmin I

Entity

1. synaptotagmin (polymer, Thiol state: all free), 152 monomers, 17324.96 Da Detail

QEKLGDICFS LRYVPTAGKL TVVILEAKNL KKMDVGGLSD PYVKIHLMQN GKRLKKKKTT IKKNTLNPYY NESFSFEVPF EQIQKVQVVV TVLDYDKIGK NDAIGKVFVG YNSTGAELRH WSDMLANPRR PIAQWHTLQV EEEVDAMLAV KK

2. CA (non-polymer), 40.078 × 2 Da

Total weight

17405.117 Da

Max. entity weight

17324.96 Da

Source organism

Rattus norvegicus

Exptl. method

NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.3 %, Completeness: 97.7 %, Completeness (bb): 97.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	97.7 % (1812 of 1855)	97.5 % (947 of 971)	98.2 % (708 of 721)	96.3 % (157 of 163)
Backbone	97.7 % (879 of 900)	97.4 % (299 of 307)	98.2 % (439 of 447)	96.6 % (141 of 146)
Sidechain	97.7 % (1073 of 1098)	97.6 % (648 of 664)	98.1 % (409 of 417)	94.1 % (16 of 17)
Aromatic	100.0 % (134 of 134)	100.0 % (67 of 67)	100.0 % (65 of 65)	100.0 % (2 of 2)
Methyl	97.8 % (180 of 184)	98.9 % (91 of 92)	96.7 % (89 of 92)

1. synaptotagmin

QEKLGDICFS LRYVPTAGKL TVVILEAKNL KKMDVGGLSD PYVKIHLMQN GKRLKKKKTT IKKNTLNPYY NESFSFEVPF EQIQKVQVVV TVLDYDKIGK NDAIGKVFVG YNSTGAELRH WSDMLANPRR PIAQWHTLQV EEEVDAMLAV KK

Show sample condition

Sample

Pressure 1 atm, Temperature 303 K, pH 6.3

#	Name	Isotope labeling	Concentration
1	synaptotagmin	[U-15N; U-13C]	1.3 mM
2	NaCl		150 mM
3	DTT		2 mM
4	MES		50 mM
5	CaCl2		20 mM
6	D2O		5 %
7	H2O		95 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type
¹H	DSS	methyl protons	0.0 ppm	external	direct
¹⁵N	nitromethane	nitrogen	-379.6 ppm	external	direct
¹³C	DSS	methyl protons	0.0 ppm	external	direct

Referencing offset: 0.02 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type
¹H	DSS	methyl protons	0.0 ppm	external	direct
¹⁵N	nitromethane	nitrogen	-379.6 ppm	external	direct
¹³C	DSS	methyl protons	0.0 ppm	external	direct

Referencing offset: 0.02 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type
¹H	DSS	methyl protons	0.0 ppm	external	direct
¹⁵N	nitromethane	nitrogen	-379.6 ppm	external	direct
¹³C	DSS	methyl protons	0.0 ppm	external	direct

Referencing offset: -0.07 ppm, Outliers: 5 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type
¹H	DSS	methyl protons	0.0 ppm	external	direct
¹⁵N	nitromethane	nitrogen	-379.6 ppm	external	direct
¹³C	DSS	methyl protons	0.0 ppm	external	direct

Referencing offset: 0.61 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 1K5W, Strand ID: A Detail

Release date

2002-02-13

Citation

Three-dimensional structure of the synaptotagmin 1 C2B-domain: synaptotagmin 1 as a phospholipid binding machine
Fernandez, I., Arac, D., Ubach, J., Gerber, S.H., Shin, O., Gao, Y., Anderson, R.G.W., Sudhof, T.C., Rizo, J.
Neuron (2001), 32, 1057-1069, PubMed 11754837 , DOI: , Abstract

Related entities 1. synaptotagmin, : 1 : 16 : 1 : 15 : 290 entities Detail

Interaction partners 1. synaptotagmin, : 27 interactors Detail

More details for 27 interactors identified by 15 citations

Experiments performed 4 experiments Detail

1 3D 15N-separated NOESY

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 303 K, pH 6.3

#	Name	Isotope labeling	Concentration
1	synaptotagmin	[U-15N; U-13C]	1.3 mM
2	NaCl		150 mM
3	DTT		2 mM
4	MES		50 mM
5	CaCl2		20 mM
6	D2O		5 %
7	H2O		95 %

Sample #2

Pressure 1 atm, Temperature 303 K, pH 6.3

#	Name	Isotope labeling	Concentration
8	synaptotagmin	[U-15N]	1.3 mM
9	NaCl		150 mM
10	DTT		2 mM
11	MES		50 mM
12	CaCl2		20 mM
13	D2O		5 %
14	H2O		95 %

Sample #3

Pressure 1 atm, Temperature 303 K, pH 6.3

#	Name	Isotope labeling	Concentration
15	synaptotagmin	[U-15N]	0.4 mM
16	NaCl		150 mM
17	DTT		2 mM
18	MES		50 mM
19	EDTA		0.5 mM
20	D2O		5 %
21	H2O		95 %

Sample #4

Pressure 1 atm, Temperature 303 K, pH 6.3

#	Name	Isotope labeling	Concentration
22	synaptotagmin	[U-10% 13C]	1 mM
23	NaCl		150 mM
24	DTT		2 mM
25	MES		50 mM
26	CaCl2		20 mM
27	D2O		5 %
28	H2O		95 %

2 3D-13C 15N-SEPARATED NOESY

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 303 K, pH 6.3

#	Name	Isotope labeling	Concentration
1	synaptotagmin	[U-15N; U-13C]	1.3 mM
2	NaCl		150 mM
3	DTT		2 mM
4	MES		50 mM
5	CaCl2		20 mM
6	D2O		5 %
7	H2O		95 %

Sample #2

Pressure 1 atm, Temperature 303 K, pH 6.3

#	Name	Isotope labeling	Concentration
8	synaptotagmin	[U-15N]	1.3 mM
9	NaCl		150 mM
10	DTT		2 mM
11	MES		50 mM
12	CaCl2		20 mM
13	D2O		5 %
14	H2O		95 %

Sample #3

Pressure 1 atm, Temperature 303 K, pH 6.3

#	Name	Isotope labeling	Concentration
15	synaptotagmin	[U-15N]	0.4 mM
16	NaCl		150 mM
17	DTT		2 mM
18	MES		50 mM
19	EDTA		0.5 mM
20	D2O		5 %
21	H2O		95 %

Sample #4

Pressure 1 atm, Temperature 303 K, pH 6.3

#	Name	Isotope labeling	Concentration
22	synaptotagmin	[U-10% 13C]	1 mM
23	NaCl		150 mM
24	DTT		2 mM
25	MES		50 mM
26	CaCl2		20 mM
27	D2O		5 %
28	H2O		95 %

3 HNHA

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 303 K, pH 6.3

#	Name	Isotope labeling	Concentration
1	synaptotagmin	[U-15N; U-13C]	1.3 mM
2	NaCl		150 mM
3	DTT		2 mM
4	MES		50 mM
5	CaCl2		20 mM
6	D2O		5 %
7	H2O		95 %

Sample #2

Pressure 1 atm, Temperature 303 K, pH 6.3

#	Name	Isotope labeling	Concentration
8	synaptotagmin	[U-15N]	1.3 mM
9	NaCl		150 mM
10	DTT		2 mM
11	MES		50 mM
12	CaCl2		20 mM
13	D2O		5 %
14	H2O		95 %

Sample #3

Pressure 1 atm, Temperature 303 K, pH 6.3

#	Name	Isotope labeling	Concentration
15	synaptotagmin	[U-15N]	0.4 mM
16	NaCl		150 mM
17	DTT		2 mM
18	MES		50 mM
19	EDTA		0.5 mM
20	D2O		5 %
21	H2O		95 %

Sample #4

Pressure 1 atm, Temperature 303 K, pH 6.3

#	Name	Isotope labeling	Concentration
22	synaptotagmin	[U-10% 13C]	1 mM
23	NaCl		150 mM
24	DTT		2 mM
25	MES		50 mM
26	CaCl2		20 mM
27	D2O		5 %
28	H2O		95 %

4 1H/13C-HSQC

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 303 K, pH 6.3

#	Name	Isotope labeling	Concentration
1	synaptotagmin	[U-15N; U-13C]	1.3 mM
2	NaCl		150 mM
3	DTT		2 mM
4	MES		50 mM
5	CaCl2		20 mM
6	D2O		5 %
7	H2O		95 %

Sample #2

Pressure 1 atm, Temperature 303 K, pH 6.3

#	Name	Isotope labeling	Concentration
8	synaptotagmin	[U-15N]	1.3 mM
9	NaCl		150 mM
10	DTT		2 mM
11	MES		50 mM
12	CaCl2		20 mM
13	D2O		5 %
14	H2O		95 %

Sample #3

Pressure 1 atm, Temperature 303 K, pH 6.3

#	Name	Isotope labeling	Concentration
15	synaptotagmin	[U-15N]	0.4 mM
16	NaCl		150 mM
17	DTT		2 mM
18	MES		50 mM
19	EDTA		0.5 mM
20	D2O		5 %
21	H2O		95 %

Sample #4

Pressure 1 atm, Temperature 303 K, pH 6.3

#	Name	Isotope labeling	Concentration
22	synaptotagmin	[U-10% 13C]	1 mM
23	NaCl		150 mM
24	DTT		2 mM
25	MES		50 mM
26	CaCl2		20 mM
27	D2O		5 %
28	H2O		95 %

nullKeywords C2B-domain, C2-domain, synaptotagmin I, calcium-binding, phospholipid-binding, synapsis, neurotransmitter release, synaptic vesicle exocytosis

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Found 1 Document (4.524 seconds)

BMRB: 5194

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. synaptotagmin, : 1 : 16 : 1 : 15 : 290 entities Detail

Interaction partners 1. synaptotagmin, : 27 interactors Detail

Experiments performed 4 experiments Detail

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