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- PDB-2m8r: Pre-Fusion Solution NMR Structure of Neuronal SNARE Syntaxin 1A -

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Basic information

Entry
Database: PDB / ID: 2m8r
TitlePre-Fusion Solution NMR Structure of Neuronal SNARE Syntaxin 1A
ComponentsSyntaxin-1A
KeywordsMEMBRANE PROTEIN / syntaxin / SNARE / Prefusion
Function / homology
Function and homology information


myosin head/neck binding / 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 / synaptic vesicle fusion to presynaptic active zone membrane / regulation of synaptic vesicle priming / Glutamate Neurotransmitter Release Cycle / positive regulation of norepinephrine secretion / Norepinephrine Neurotransmitter Release Cycle ...myosin head/neck binding / 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 / synaptic vesicle fusion to presynaptic active zone membrane / regulation of synaptic vesicle priming / Glutamate Neurotransmitter Release Cycle / positive regulation of norepinephrine secretion / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / positive regulation of catecholamine secretion / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / Dopamine Neurotransmitter Release Cycle / regulated exocytosis / synaptic vesicle docking / response to gravity / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / vesicle docking / positive regulation of calcium ion-dependent exocytosis / chloride channel inhibitor activity / secretion by cell / SNARE complex / SNAP receptor activity / LGI-ADAM interactions / hormone secretion / calcium-ion regulated exocytosis / actomyosin / regulation of exocytosis / protein localization to membrane / ATP-dependent protein binding / neurotransmitter transport / insulin secretion / SNARE complex assembly / positive regulation of neurotransmitter secretion / myosin binding / exocytosis / synaptic vesicle exocytosis / positive regulation of exocytosis / modulation of excitatory postsynaptic potential / positive regulation of excitatory postsynaptic potential / protein sumoylation / synaptic vesicle endocytosis / calcium channel inhibitor activity / endomembrane system / presynaptic active zone membrane / SNARE binding / acrosomal vesicle / secretory granule / postsynaptic density membrane / intracellular protein transport / Schaffer collateral - CA1 synapse / synaptic vesicle membrane / kinase binding / calcium-dependent protein binding / synaptic vesicle / presynapse / protein-macromolecule adaptor activity / presynaptic membrane / nuclear membrane / transmembrane transporter binding / postsynaptic density / neuron projection / axon / glutamatergic synapse / synapse / protein-containing complex binding / protein-containing complex / identical protein binding / membrane / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / Syntaxin / SNARE domain / Syntaxin/epimorphin, conserved site / Syntaxin / epimorphin family signature. / SNARE / Helical region found in SNAREs ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / Syntaxin / SNARE domain / Syntaxin/epimorphin, conserved site / Syntaxin / epimorphin family signature. / SNARE / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / distance geometry, simulated annealing
Model detailslowest energy, model20
AuthorsLiang, B. / Kiessling, V. / Tamm, L.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Prefusion structure of syntaxin-1A suggests pathway for folding into neuronal trans-SNARE complex fusion intermediate.
Authors: Liang, B. / Kiessling, V. / Tamm, L.K.
History
DepositionMay 24, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Dec 11, 2013Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Syntaxin-1A


Theoretical massNumber of molelcules
Total (without water)12,3341
Polymers12,3341
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #20lowest energy

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Components

#1: Protein Syntaxin-1A / Neuron-specific antigen HPC-1 / Synaptotagmin-associated 35 kDa protein / P35A


Mass: 12334.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stx1a, Sap / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P32851

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1313D HNCO
1413D HNCA
1513D HN(CA)CB
1613D HN(CO)CA
1723D HNHA
1823D (H)CCH-TOCSY
1923D (H)CCH-COSY
11023D H(CCO)NH
11123D C(CO)NH
11222D 1H-13C HSQC aromatic
11322D 1H-13C HSQC aliphatic
11423D 1H-15N NOESY
11523D 1H-13C NOESY
11613D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-13C; U-15N; U-2H] syntaxin, 100 mM DPC, 10 mM HEPES, 10 mM MES, 10 mM sodium acetate, 150 mM sodium chloride, 5 mM DTT, 1 mM EDTA, 95% H2O/5% D2O95% H2O/5% D2O
21 mM [U-100% 13C; U-100% 15N] syntaxin, 100 mM [U-99% 2H] DPC, 150 mM sodium chloride, 0.02 % sodium azide, 10 mM sodium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity-1[U-13C; U-15N; U-2H]1
100 mMDPC-21
10 mMHEPES-31
10 mMMES-41
10 mMsodium acetate-51
150 mMsodium chloride-61
5 mMDTT-71
1 mMEDTA-81
1 mMentity-9[U-100% 13C; U-100% 15N]2
100 mMDPC-10[U-99% 2H]2
150 mMsodium chloride-112
0.02 %sodium azide-122
10 mMsodium phosphate-132
Sample conditionspH: 5.5 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.32Schwieters, Kuszewski, Tjandra and Clorestructure solution
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
TopSpinBruker Biospincollection
X-PLOR NIH2.32Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1085 / NOE intraresidue total count: 512 / NOE long range total count: 6 / NOE medium range total count: 218 / NOE sequential total count: 349 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 34 / Protein phi angle constraints total count: 91 / Protein psi angle constraints total count: 91
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20
NMR ensemble rmsDistance rms dev: 0.033 Å / Distance rms dev error: 0.002 Å

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