BMRB Entry 34738

Name: Phosphatidylserine-dependent synaptic vesicle membrane sculpting by synaptogyrin
Published: 2023-05-19

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PDB ID: 8a6m
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34738
MolProbity Validation Chart

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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Phosphatidylserine-dependent synaptic vesicle membrane sculpting by synaptogyrin

Deposition date:

2022-06-18

Original release date:

2023-05-19

Authors:

Yu, T.; Eastep, G.; Flores, D.; Zweckstetter, M.

Citation:

Citation: Yu, Taekyung; Flores-Solis, David; Eastep, Gunnar; Becker, Stefan; Zweckstetter, Markus. "Phosphatidylserine-dependent structure of synaptogyrin remodels the synaptic vesicle membrane" Nat. Struct. Mol. Biol. 30, 926-934 (2023).
PubMed: 37217654

Assembly members:

Assembly members:
entity_1, polymer, 210 residues, 23356.428 Da.

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MGHHHHHHHASENLYFQGHM EGGAYGAGKAGGAFDPYTLV RQPHTILRVVSWLFSIVVFG SIVNEGYLNSASEGEEFCIY NRNPNACSYGVAVGVLAFLT CLLYLALDVYFPQISSVKDR KKAVLSDIGVSAFWAFLWFV GFCYLANQWQVSKPKDNPLN EGTDAARAAIAFSFFSIFTW SLTAALAVRRFKDLSFQEEY STLFPASAQP

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	561
15N chemical shifts	182
1H chemical shifts	1222

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 210 residues - 23356.428 Da.

1	MET	GLY	HIS	HIS	HIS	HIS	HIS	HIS	HIS	ALA
2	SER	GLU	ASN	LEU	TYR	PHE	GLN	GLY	HIS	MET
3	GLU	GLY	GLY	ALA	TYR	GLY	ALA	GLY	LYS	ALA
4	GLY	GLY	ALA	PHE	ASP	PRO	TYR	THR	LEU	VAL
5	ARG	GLN	PRO	HIS	THR	ILE	LEU	ARG	VAL	VAL
6	SER	TRP	LEU	PHE	SER	ILE	VAL	VAL	PHE	GLY
7	SER	ILE	VAL	ASN	GLU	GLY	TYR	LEU	ASN	SER
8	ALA	SER	GLU	GLY	GLU	GLU	PHE	CYS	ILE	TYR
9	ASN	ARG	ASN	PRO	ASN	ALA	CYS	SER	TYR	GLY
10	VAL	ALA	VAL	GLY	VAL	LEU	ALA	PHE	LEU	THR
11	CYS	LEU	LEU	TYR	LEU	ALA	LEU	ASP	VAL	TYR
12	PHE	PRO	GLN	ILE	SER	SER	VAL	LYS	ASP	ARG
13	LYS	LYS	ALA	VAL	LEU	SER	ASP	ILE	GLY	VAL
14	SER	ALA	PHE	TRP	ALA	PHE	LEU	TRP	PHE	VAL
15	GLY	PHE	CYS	TYR	LEU	ALA	ASN	GLN	TRP	GLN
16	VAL	SER	LYS	PRO	LYS	ASP	ASN	PRO	LEU	ASN
17	GLU	GLY	THR	ASP	ALA	ALA	ARG	ALA	ALA	ILE
18	ALA	PHE	SER	PHE	PHE	SER	ILE	PHE	THR	TRP
19	SER	LEU	THR	ALA	ALA	LEU	ALA	VAL	ARG	ARG
20	PHE	LYS	ASP	LEU	SER	PHE	GLN	GLU	GLU	TYR
21	SER	THR	LEU	PHE	PRO	ALA	SER	ALA	GLN	PRO

Samples:

sample_1: Synaptogyrin 1b, [U-15N], 0.8 mM

sample_2: Synaptogyrin 1b, [U-13C; U-15N; U-2H], 0.8 mM

sample_3: Synaptogyrin 1b, [U-15N; U-2H], 0.8 mM

sample_4: Synaptogyrin 1b, [U-100% 13C; U-100% 15N], 0.8 mM

sample_5: Synaptogyrin 1b, [U-15N], 0.8 mM

sample_conditions_1: ionic strength: 20 mM; pH: 8.5; pressure: 1 atm; temperature: 313 K

sample_conditions_2: ionic strength: 20 mM; pH: 8.5; pressure: 1 atm; temperature: 313 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	anisotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_4	anisotropic	sample_conditions_1
3D HNCO	sample_2	anisotropic	sample_conditions_1
3D HN(CA)CO	sample_2	anisotropic	sample_conditions_1
3D HNCA	sample_2	anisotropic	sample_conditions_1
3D HN(CO)CA	sample_2	anisotropic	sample_conditions_1
3D HNCACB	sample_3	anisotropic	sample_conditions_1
3D HNCB	sample_3	anisotropic	sample_conditions_1
3D 1H-13C NOESY	sample_4	anisotropic	sample_conditions_2
3D 1H-15N NOESY	sample_3	anisotropic	sample_conditions_2
3D 1H-15N NOESY	sample_5	anisotropic	sample_conditions_2

Software:

CcpNmr Analysis, CCPN - chemical shift assignment

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

CYANA, Guntert, Mumenthaler and Wuthrich - peak picking

CS-ROSETTA, Shen, Vernon, Baker and Bax - structure calculation

NMR spectrometers:

Bruker AVANCE III HD 950 MHz
Bruker AVANCE III HD 900 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks

1	MET	GLY	HIS	HIS	HIS	HIS	HIS	HIS	HIS	ALA
2	SER	GLU	ASN	LEU	TYR	PHE	GLN	GLY	HIS	MET
3	GLU	GLY	GLY	ALA	TYR	GLY	ALA	GLY	LYS	ALA
4	GLY	GLY	ALA	PHE	ASP	PRO	TYR	THR	LEU	VAL
5	ARG	GLN	PRO	HIS	THR	ILE	LEU	ARG	VAL	VAL
6	SER	TRP	LEU	PHE	SER	ILE	VAL	VAL	PHE	GLY
7	SER	ILE	VAL	ASN	GLU	GLY	TYR	LEU	ASN	SER
8	ALA	SER	GLU	GLY	GLU	GLU	PHE	CYS	ILE	TYR
9	ASN	ARG	ASN	PRO	ASN	ALA	CYS	SER	TYR	GLY
10	VAL	ALA	VAL	GLY	VAL	LEU	ALA	PHE	LEU	THR
11	CYS	LEU	LEU	TYR	LEU	ALA	LEU	ASP	VAL	TYR
12	PHE	PRO	GLN	ILE	SER	SER	VAL	LYS	ASP	ARG
13	LYS	LYS	ALA	VAL	LEU	SER	ASP	ILE	GLY	VAL
14	SER	ALA	PHE	TRP	ALA	PHE	LEU	TRP	PHE	VAL
15	GLY	PHE	CYS	TYR	LEU	ALA	ASN	GLN	TRP	GLN
16	VAL	SER	LYS	PRO	LYS	ASP	ASN	PRO	LEU	ASN
17	GLU	GLY	THR	ASP	ALA	ALA	ARG	ALA	ALA	ILE
18	ALA	PHE	SER	PHE	PHE	SER	ILE	PHE	THR	TRP
19	SER	LEU	THR	ALA	ALA	LEU	ALA	VAL	ARG	ARG
20	PHE	LYS	ASP	LEU	SER	PHE	GLN	GLU	GLU	TYR
21	SER	THR	LEU	PHE	PRO	ALA	SER	ALA	GLN	PRO

1	MET	GLY	HIS	HIS	HIS	HIS	HIS	HIS	HIS	ALA
2	SER	GLU	ASN	LEU	TYR	PHE	GLN	GLY	HIS	MET
3	GLU	GLY	GLY	ALA	TYR	GLY	ALA	GLY	LYS	ALA
4	GLY	GLY	ALA	PHE	ASP	PRO	TYR	THR	LEU	VAL
5	ARG	GLN	PRO	HIS	THR	ILE	LEU	ARG	VAL	VAL
6	SER	TRP	LEU	PHE	SER	ILE	VAL	VAL	PHE	GLY
7	SER	ILE	VAL	ASN	GLU	GLY	TYR	LEU	ASN	SER
8	ALA	SER	GLU	GLY	GLU	GLU	PHE	CYS	ILE	TYR
9	ASN	ARG	ASN	PRO	ASN	ALA	CYS	SER	TYR	GLY
10	VAL	ALA	VAL	GLY	VAL	LEU	ALA	PHE	LEU	THR
11	CYS	LEU	LEU	TYR	LEU	ALA	LEU	ASP	VAL	TYR
12	PHE	PRO	GLN	ILE	SER	SER	VAL	LYS	ASP	ARG
13	LYS	LYS	ALA	VAL	LEU	SER	ASP	ILE	GLY	VAL
14	SER	ALA	PHE	TRP	ALA	PHE	LEU	TRP	PHE	VAL
15	GLY	PHE	CYS	TYR	LEU	ALA	ASN	GLN	TRP	GLN
16	VAL	SER	LYS	PRO	LYS	ASP	ASN	PRO	LEU	ASN
17	GLU	GLY	THR	ASP	ALA	ALA	ARG	ALA	ALA	ILE
18	ALA	PHE	SER	PHE	PHE	SER	ILE	PHE	THR	TRP
19	SER	LEU	THR	ALA	ALA	LEU	ALA	VAL	ARG	ARG
20	PHE	LYS	ASP	LEU	SER	PHE	GLN	GLU	GLU	TYR
21	SER	THR	LEU	PHE	PRO	ALA	SER	ALA	GLN	PRO

1	MET	GLY	HIS	HIS	HIS	HIS	HIS	HIS	HIS	ALA
2	SER	GLU	ASN	LEU	TYR	PHE	GLN	GLY	HIS	MET
3	GLU	GLY	GLY	ALA	TYR	GLY	ALA	GLY	LYS	ALA
4	GLY	GLY	ALA	PHE	ASP	PRO	TYR	THR	LEU	VAL
5	ARG	GLN	PRO	HIS	THR	ILE	LEU	ARG	VAL	VAL
6	SER	TRP	LEU	PHE	SER	ILE	VAL	VAL	PHE	GLY
7	SER	ILE	VAL	ASN	GLU	GLY	TYR	LEU	ASN	SER
8	ALA	SER	GLU	GLY	GLU	GLU	PHE	CYS	ILE	TYR
9	ASN	ARG	ASN	PRO	ASN	ALA	CYS	SER	TYR	GLY
10	VAL	ALA	VAL	GLY	VAL	LEU	ALA	PHE	LEU	THR
11	CYS	LEU	LEU	TYR	LEU	ALA	LEU	ASP	VAL	TYR
12	PHE	PRO	GLN	ILE	SER	SER	VAL	LYS	ASP	ARG
13	LYS	LYS	ALA	VAL	LEU	SER	ASP	ILE	GLY	VAL
14	SER	ALA	PHE	TRP	ALA	PHE	LEU	TRP	PHE	VAL
15	GLY	PHE	CYS	TYR	LEU	ALA	ASN	GLN	TRP	GLN
16	VAL	SER	LYS	PRO	LYS	ASP	ASN	PRO	LEU	ASN
17	GLU	GLY	THR	ASP	ALA	ALA	ARG	ALA	ALA	ILE
18	ALA	PHE	SER	PHE	PHE	SER	ILE	PHE	THR	TRP
19	SER	LEU	THR	ALA	ALA	LEU	ALA	VAL	ARG	ARG
20	PHE	LYS	ASP	LEU	SER	PHE	GLN	GLU	GLU	TYR
21	SER	THR	LEU	PHE	PRO	ALA	SER	ALA	GLN	PRO