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- PDB-2kog: lipid-bound synaptobrevin solution NMR structure -

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Basic information

Entry
Database: PDB / ID: 2kog
Titlelipid-bound synaptobrevin solution NMR structure
ComponentsVesicle-associated membrane protein 2Vesicle-associated membrane protein
KeywordsMEMBRANE PROTEIN / synaptobrevin / VAMP2 / DPC micelle / SNARE / Coiled coil / Membrane fusion / Transmembrane / Synaptic vesicle
Function / homology
Function and homology information


trans-Golgi Network Vesicle Budding / regulation of delayed rectifier potassium channel activity / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / Lysosome Vesicle Biogenesis / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle ...trans-Golgi Network Vesicle Budding / regulation of delayed rectifier potassium channel activity / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / Lysosome Vesicle Biogenesis / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / zymogen granule membrane / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / regulated exocytosis / Dopamine Neurotransmitter Release Cycle / Golgi Associated Vesicle Biogenesis / storage vacuole / synaptic vesicle docking / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / eosinophil degranulation / vesicle fusion / SNARE complex / Golgi to plasma membrane protein transport / SNAP receptor activity / regulation of vesicle-mediated transport / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / hormone secretion / calcium-ion regulated exocytosis / positive regulation of intracellular protein transport / regulation of exocytosis / neuron projection terminus / regulation of synaptic vesicle recycling / syntaxin-1 binding / SNARE complex assembly / syntaxin binding / clathrin-coated vesicle / myosin binding / synaptic vesicle exocytosis / synaptic vesicle endocytosis / response to glucose / vesicle-mediated transport / SNARE binding / secretory granule / long-term synaptic potentiation / establishment of localization in cell / phospholipid binding / cytoplasmic vesicle membrane / trans-Golgi network / terminal bouton / synaptic vesicle membrane / cellular response to insulin stimulus / calcium-dependent protein binding / synaptic vesicle / cytoplasmic vesicle / protein-containing complex assembly / vesicle / transmembrane transporter binding / membrane fusion / molecular adaptor activity / calmodulin binding / synapse / lipid binding / protein-containing complex binding / perinuclear region of cytoplasm / membrane / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Synaptobrevin/Vesicle-associated membrane protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin signature. / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Vesicle-associated membrane protein 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsEllena, J.F. / Liang, B. / Wiktor, M. / Stein, A. / Cafiso, D.S. / Jahn, R. / Tamm, L.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Dynamic structure of lipid-bound synaptobrevin suggests a nucleation-propagation mechanism for trans-SNARE complex formation.
Authors: Ellena, J.F. / Liang, B. / Wiktor, M. / Stein, A. / Cafiso, D.S. / Jahn, R. / Tamm, L.K.
History
DepositionSep 22, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vesicle-associated membrane protein 2


Theoretical massNumber of molelcules
Total (without water)12,9861
Polymers12,9861
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Vesicle-associated membrane protein 2 / Vesicle-associated membrane protein / VAMP-2 / Synaptobrevin-2


Mass: 12986.014 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vamp2, Syb2 / Production host: Escherichia coli (E. coli) / References: UniProt: P63045

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: full-length rat synaptobrevin structure in DPC micelles
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CA)CB
1413D HNCO
1513D HN(CA)CO
1613D CBCA(CO)NH
1713D HNHA
1813D 1H-15N NOESY
1913D H(CCO)NH
11013D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 1 mM [U-99% 13C; U-99% 15N] synaptobrevin-1, 200 mM DPC-2, 20 mM MES-3, 150 mM NaCl-4, 5 mM DTT-5, 1 mM EDTA-6, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMsynaptobrevin-1[U-99% 13C; U-99% 15N]1
200 mMDPC-21
20 mMMES-31
150 mMNaCl-41
5 mMDTT-51
1 mMEDTA-61
Sample conditionsIonic strength: 150 / pH: 6 / Pressure: ambient / Temperature: 318 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE6003

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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