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- PDB-6wvw: Crystal structure of the R59P-SNAP25 containing SNARE complex -

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Basic information

Entry
Database: PDB / ID: 6wvw
TitleCrystal structure of the R59P-SNAP25 containing SNARE complex
Components
  • (Synaptosomal-associated protein ...) x 2
  • Syntaxin-1A
  • Vesicle-associated membrane protein 2
KeywordsEXOCYTOSIS / SNARE complex / synaptic vesicle fusion
Function / homology
Function and homology information


exocytic insertion of neurotransmitter receptor to postsynaptic membrane / trans-Golgi Network Vesicle Budding / regulation of delayed rectifier potassium channel activity / BLOC-1 complex / myosin head/neck binding / Lysosome Vesicle Biogenesis / zymogen granule membrane / synaptic vesicle fusion to presynaptic active zone membrane / storage vacuole / Other interleukin signaling ...exocytic insertion of neurotransmitter receptor to postsynaptic membrane / trans-Golgi Network Vesicle Budding / regulation of delayed rectifier potassium channel activity / BLOC-1 complex / myosin head/neck binding / Lysosome Vesicle Biogenesis / zymogen granule membrane / synaptic vesicle fusion to presynaptic active zone membrane / storage vacuole / Other interleukin signaling / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / presynaptic dense core vesicle exocytosis / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / extrinsic component of presynaptic membrane / calcium ion-regulated exocytosis of neurotransmitter / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / positive regulation of catecholamine secretion / positive regulation of norepinephrine secretion / Dopamine Neurotransmitter Release Cycle / synaptic vesicle docking / eosinophil degranulation / Golgi Associated Vesicle Biogenesis / regulation of synaptic vesicle priming / regulated exocytosis / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / vesicle-mediated transport in synapse / regulation of establishment of protein localization / positive regulation of calcium ion-dependent exocytosis / ribbon synapse / positive regulation of intracellular protein transport / regulation of vesicle-mediated transport / vesicle docking / Cargo recognition for clathrin-mediated endocytosis / chloride channel inhibitor activity / secretion by cell / regulation of exocytosis / Clathrin-mediated endocytosis / SNARE complex / SNAP receptor activity / calcium-ion regulated exocytosis / vesicle fusion / actomyosin / hormone secretion / LGI-ADAM interactions / positive regulation of hormone secretion / Golgi to plasma membrane protein transport / ATP-dependent protein binding / neurotransmitter secretion / protein localization to membrane / clathrin-coated vesicle / syntaxin binding / syntaxin-1 binding / regulation of synaptic vesicle recycling / insulin secretion / Neutrophil degranulation / endosomal transport / SNARE complex assembly / positive regulation of neurotransmitter secretion / neurotransmitter transport / myosin binding / regulation of synapse assembly / response to gravity / regulation of neuron projection development / synaptic vesicle priming / exocytosis / neuron projection terminus / positive regulation of exocytosis / protein sumoylation / synaptic vesicle exocytosis / modulation of excitatory postsynaptic potential / voltage-gated potassium channel activity / associative learning / synaptic vesicle endocytosis / long-term memory / postsynaptic cytosol / response to glucose / axonal growth cone / calcium channel inhibitor activity / vesicle-mediated transport / somatodendritic compartment / voltage-gated potassium channel complex / photoreceptor inner segment / presynaptic active zone membrane / endomembrane system / acrosomal vesicle / axonogenesis / secretory granule / cytoplasmic vesicle membrane / positive regulation of excitatory postsynaptic potential / SNARE binding / filopodium / establishment of localization in cell / intracellular protein transport / locomotory behavior / trans-Golgi network
Similarity search - Function
Synaptobrevin/Vesicle-associated membrane protein / Synaptobrevin signature. / Synaptosomal-associated protein 25 / SNAP-25 domain / Synaptobrevin-like / SNAP-25 family / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Syntaxin ...Synaptobrevin/Vesicle-associated membrane protein / Synaptobrevin signature. / Synaptosomal-associated protein 25 / SNAP-25 domain / Synaptobrevin-like / SNAP-25 family / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / SNARE domain / Syntaxin / 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
Similarity search - Domain/homology
Syntaxin-1A / Synaptosomal-associated protein 25 / Vesicle-associated membrane protein 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsZhou, Q. / White, K.I. / Brunger, A.T.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R37MH63105 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)K99MH113764 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R00MH113764 United States
CitationJournal: Neuron / Year: 2021
Title: Role of Aberrant Spontaneous Neurotransmission in SNAP25-Associated Encephalopathies.
Authors: Alten, B. / Zhou, Q. / Shin, O.H. / Esquivies, L. / Lin, P.Y. / White, K.I. / Sun, R. / Chung, W.K. / Monteggia, L.M. / Brunger, A.T. / Kavalali, E.T.
History
DepositionMay 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vesicle-associated membrane protein 2
B: Syntaxin-1A
C: Synaptosomal-associated protein 25
D: Synaptosomal-associated protein 25
E: Vesicle-associated membrane protein 2
F: Syntaxin-1A
G: Synaptosomal-associated protein 25
H: Synaptosomal-associated protein 25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,08814
Polymers61,6918
Non-polymers3976
Water4,756264
1
A: Vesicle-associated membrane protein 2
B: Syntaxin-1A
C: Synaptosomal-associated protein 25
D: Synaptosomal-associated protein 25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0447
Polymers30,8464
Non-polymers1983
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12870 Å2
ΔGint-146 kcal/mol
Surface area13980 Å2
MethodPISA
2
E: Vesicle-associated membrane protein 2
F: Syntaxin-1A
G: Synaptosomal-associated protein 25
H: Synaptosomal-associated protein 25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0447
Polymers30,8464
Non-polymers1983
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12230 Å2
ΔGint-126 kcal/mol
Surface area13760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.761, 45.899, 109.066
Angle α, β, γ (deg.)90.000, 94.410, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 2 types, 4 molecules AEBF

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


Mass: 7231.061 Da / Num. of mol.: 2
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
#2: Protein Syntaxin-1A / Neuron-specific antigen HPC-1 / Synaptotagmin-associated 35 kDa protein / P35A


Mass: 7706.761 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stx1a, Sap / Production host: Escherichia coli (E. coli) / References: UniProt: P32851

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Synaptosomal-associated protein ... , 2 types, 4 molecules CGDH

#3: Protein Synaptosomal-associated protein 25 / SNAP-25 / Super protein / SUP / Synaptosomal-associated 25 kDa protein


Mass: 8567.544 Da / Num. of mol.: 2 / Mutation: R59P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Snap25, Snap / Production host: Escherichia coli (E. coli) / References: UniProt: P60881
#4: Protein Synaptosomal-associated protein 25 / SNAP-25 / Super protein / SUP / Synaptosomal-associated 25 kDa protein


Mass: 7340.173 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Snap25, Snap / Production host: Escherichia coli (E. coli) / References: UniProt: P60881

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Non-polymers , 3 types, 270 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 100 mM MES (pH 6.0), 100 mM CaCl2, 20-25% (v/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.11→42.29 Å / Num. obs: 19820 / % possible obs: 89.6 % / Redundancy: 11.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.155 / Net I/σ(I): 11.2
Reflection shellResolution: 2.11→2.186 Å / Num. unique obs: 498 / CC1/2: 0.374

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Processing

Software
NameVersionClassification
PHENIX1.18refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N7S

1n7s


Resolution: 2.11→42.29 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.244 --
Rwork0.2003 --
obs-19820 89.6 %
Displacement parametersBiso mean: 34.58 Å2
Refinement stepCycle: LAST / Resolution: 2.11→42.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4224 0 20 264 4508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00524395
X-RAY DIFFRACTIONf_angle_d0.68045897
X-RAY DIFFRACTIONf_chiral_restr0.0314653
X-RAY DIFFRACTIONf_plane_restr0.0074807
X-RAY DIFFRACTIONf_dihedral_angle_d24.54361775
LS refinement shellResolution: 2.11→2.186 Å
RfactorNum. reflection% reflection
Rfree0.3445 --
Rwork0.2619 --
obs-498 58.2 %

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