BMRB Entry 34738
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PDB ID:
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
NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry
Title: Phosphatidylserine-dependent synaptic vesicle membrane sculpting by synaptogyrin PubMed: 37217654
Deposition date: 2022-06-18 Original release date: 2023-05-19
Authors: Yu, T.; Eastep, G.; Flores, D.; Zweckstetter, M.
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).
Assembly members:
entity_1, polymer, 210 residues, 23356.428 Da.
Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
entity_1: MGHHHHHHHASENLYFQGHM
EGGAYGAGKAGGAFDPYTLV
RQPHTILRVVSWLFSIVVFG
SIVNEGYLNSASEGEEFCIY
NRNPNACSYGVAVGVLAFLT
CLLYLALDVYFPQISSVKDR
KKAVLSDIGVSAFWAFLWFV
GFCYLANQWQVSKPKDNPLN
EGTDAARAAIAFSFFSIFTW
SLTAALAVRRFKDLSFQEEY
STLFPASAQP
- assigned_chemical_shifts
Data type | Count |
13C chemical shifts | 561 |
15N chemical shifts | 182 |
1H chemical shifts | 1222 |
Additional metadata:
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 shifts
SPARKY: Backbone
or all simulated shifts