BMRB: 11314

Solution Structure of the RING domain of the Synaptotagmin-like protein 4

Authors

Miyamoto, K., Sato, M., Koshiba, S., Inoue, M., Kigawa, T., Yokoyama, S.

Assembly

Synaptotagmin-like protein 4

Entity

1. RING domain (polymer, Thiol state: all other bound), 76 monomers, 8204.175 Da Detail

GSSGSSGLLE IKRKGAKRGS QHYSDRTCAR CQESLGRLSP KTNTCRGCNH LVCRDCRIQE SNGTWRCKVC SGPSSG

2. ZN (non-polymer), 65.409 × 2 Da

Total weight

8334.993 Da

Max. entity weight

8204.175 Da

Entity Connection

na 8 Detail

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ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS28:SG	2:ZN1:ZN
2	na	sing	1:CYS31:SG	2:ZN1:ZN
3	na	sing	1:CYS53:SG	2:ZN1:ZN
4	na	sing	1:CYS56:SG	2:ZN1:ZN
5	na	sing	1:CYS45:SG	2:ZN1:ZN
6	na	sing	1:CYS48:SG	2:ZN1:ZN
7	na	sing	1:CYS67:SG	2:ZN1:ZN
8	na	sing	1:CYS70:SG	2:ZN1:ZN

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.7 %, Completeness: 89.6 %, Completeness (bb): 88.1 % Detail

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Polymer type: polypeptide(L)

	Total	1H	13C	15N
All	89.6 % (733 of 818)	88.7 % (385 of 434)	91.4 % (277 of 303)	87.7 % (71 of 81)
Backbone	88.1 % (398 of 452)	87.5 % (140 of 160)	89.0 % (194 of 218)	86.5 % (64 of 74)
Sidechain	90.3 % (390 of 432)	88.0 % (241 of 274)	94.0 % (142 of 151)	100.0 % (7 of 7)
Aromatic	100.0 % (28 of 28)	100.0 % (14 of 14)	100.0 % (13 of 13)	100.0 % (1 of 1)
Methyl	100.0 % (48 of 48)	100.0 % (24 of 24)	100.0 % (24 of 24)

1. RING domain

GSSGSSGLLE IKRKGAKRGS QHYSDRTCAR CQESLGRLSP KTNTCRGCNH LVCRDCRIQE SNGTWRCKVC SGPSSG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 (±0.001) atm, Temperature 296 (±0.1) K, pH 7.0 (±0.05), Details 1.37mM RING domain {U-13C,15N;} 20mM {d-Tris-HCl(pH7.0);} 100mM {NaCl;} 1mM {d-DTT;} 0.02% {NaN3;} 0.05mM {ZNCl2;} 0.1mM {NTA;} 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	RING domain	[U-13C; U-15N]	protein	1.37 mM
2	d-Tris-HCl	natural abundance	buffer	20 mM
3	NaCl	natural abundance	salt	100 mM
4	d-DTT	natural abundance	salt	1 mM
5	NaN3	natural abundance	salt	0.02 %
6	ZnCl2	natural abundance	salt	0.05 mM
7	NTA	natural abundance	salt	0.1 mM
8	H2O		solvent	90 %
9	D2O		solvent	10 %

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LACS Plot; CA

Referencing offset: -0.13 ppm, Outliers: 1 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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LACS Plot; CB

Referencing offset: -0.13 ppm, Outliers: 1 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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LACS Plot; HA

Referencing offset: -0.01 ppm, Outliers: 1 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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LACS Plot; CO

Referencing offset: 0.02 ppm, Outliers: 1 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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Protein Blocks Logo

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

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Release date

2011-08-18

Citation

The unique N-terminal zinc finger of Synaptotagmin-like protein 4 reveals FYVE structure
Miyamoto, K., Sato, M., Koshiba, S., Inoue, M., Kigawa, T., Yokoyama, S.
Protein Sci. (2017), PubMed 28906046 , DOI 10.1002/pro.3301 , Abstract

Related entities 1. RING domain, : 1 : 36 entities Detail

Interaction partners 1. RING domain, : 8 interactors Detail

Experiments performed 2 experiments Detail