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- PDB-8a6m: Phosphatidylserine-dependent synaptic vesicle membrane sculpting ... -

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Basic information

Entry
Database: PDB / ID: 8a6m
TitlePhosphatidylserine-dependent synaptic vesicle membrane sculpting by synaptogyrin
ComponentsIsoform 1B of Synaptogyrin-1
KeywordsMEMBRANE PROTEIN / Tetraspan vesicle membrane protein
Function / homology
Function and homology information


synaptic vesicle membrane organization / regulated exocytosis / regulation of short-term neuronal synaptic plasticity / azurophil granule membrane / protein targeting / cellular response to leukemia inhibitory factor / regulation of long-term neuronal synaptic plasticity / neuromuscular junction / synaptic vesicle membrane / melanosome ...synaptic vesicle membrane organization / regulated exocytosis / regulation of short-term neuronal synaptic plasticity / azurophil granule membrane / protein targeting / cellular response to leukemia inhibitory factor / regulation of long-term neuronal synaptic plasticity / neuromuscular junction / synaptic vesicle membrane / melanosome / Neutrophil degranulation / membrane / plasma membrane
Similarity search - Function
Synaptogyrin / Marvel domain / Membrane-associating domain / MARVEL domain profile.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry
AuthorsYu, T.K. / Eastep, G.N. / Flores, D. / Zweckstetter, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)105286809 Germany
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2023
Title: Phosphatidylserine-dependent structure of synaptogyrin remodels the synaptic vesicle membrane.
Authors: Yu, T. / Flores-Solis, D. / Eastep, G.N. / Becker, S. / Zweckstetter, M.
History
DepositionJun 18, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 1B of Synaptogyrin-1


Theoretical massNumber of molelcules
Total (without water)23,3561
Polymers23,3561
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 470structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Isoform 1B of Synaptogyrin-1


Mass: 23356.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYNGR1 / Production host: Escherichia coli (E. coli) / References: UniProt: O43759

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D 1H-15N HSQC
125anisotropic12D 1H-13C HSQC aliphatic
133anisotropic13D HNCO
143anisotropic13D HN(CA)CO
153anisotropic13D HNCA
163anisotropic13D HN(CO)CA
173anisotropic13D HN(CA)CB
183anisotropic13D HNCB
2104anisotropic23D 1H-15N NOESY
295anisotropic23D 1H-13C NOESY
2116anisotropic23D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
micelle10.8 mM [U-15N] Synaptogyrin 1b, 90% H2O/10% D2O20mM potassium phosphate, 150mM NaCl, 1mM TCEP, 0.1% UDM1H,15N_sample90% H2O/10% D2O
micelle30.8 mM [U-13C; U-15N; U-2H] Synaptogyrin 1b, 90% H2O/10% D2O20mM potassium phosphate, 150mM NaCl, 1mM TCEP, 0.1% UDM1H,13C,15N_sample90% H2O/10% D2O
micelle40.8 mM [U-15N; U-2H] Synaptogyrin 1b, 100% D2O20mM potassium phosphate, 150mM NaCl, 1mM TCEP, 0.03% d25-DDM1H,15N_sample100% D2O
micelle50.8 mM [U-100% 13C; U-100% 15N] Synaptogyrin 1b, 100% D2O20mM potassium phosphate, 150mM NaCl, 1mM TCEP, 0.03% d25-DDM13C,15N_sample100% D2O
micelle60.8 mM [U-15N] Synaptogyrin 1b, 100% D2O20mM potassium phosphate, 150mM NaCl, 1mM TCEP, 0.03% d25-DDM15N_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMSynaptogyrin 1b[U-15N]1
0.8 mMSynaptogyrin 1b[U-13C; U-15N; U-2H]3
0.8 mMSynaptogyrin 1b[U-15N; U-2H]4
0.8 mMSynaptogyrin 1b[U-100% 13C; U-100% 15N]5
0.8 mMSynaptogyrin 1b[U-15N]6
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
120 mMUDM micelle8.5 ambient Pa313 K
220 mMd25-DDM micelle8.5 ambient Pa313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE III HDBrukerAVANCE III HD9501
Bruker AVANCE III HDBrukerAVANCE III HD9002

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Processing

NMR software
NameDeveloperClassification
CcpNmr AnalysisCCPNchemical shift assignment
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAGuntert, Mumenthaler and Wuthrichpeak picking
CS-ROSETTAShen, Vernon, Baker and Baxstructure calculation
RefinementMethod: distance geometry / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 470 / Conformers submitted total number: 10

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